Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.86	0.93	0.89	12963	1798	2037	228	12
INDEL	1 - 100	0.68	0.91	0.78	9434	224	4462	126	18
SV	ALL	0.86	0.93	0.89	2910	37	461	2744	140

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.86	0.93	0.89	12963	1798	2037	228	12
INDEL	1 - 100	0.68	0.91	0.78	9434	224	4462	126	18
TRA	TRA	0.78	0.88	0.83	576	12	160	250	22
INV	> 0	0.86	0.99	0.92	572	2	95	435	21
DEL	> 100	0.91	0.88	0.89	1198	22	120	1086	68
DUP	> 100	0.87	0.99	0.92	564	1	86	1217	50

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.86	0.93	0.89	12963	1798	2037	228	12
INDEL	1 - 100	0.68	0.91	0.78	9434	224	4462	126	18
TRA	TRA	0.78	0.88	0.83	576	12	160	250	22
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	0.0	1.0	0.0	0	0	0	0	0
INV	> 500	0.86	0.98	0.92	572	2	95	435	21
DEL	101 - 500	0.87	0.51	0.65	255	19	37	121	10
DEL	> 500	0.92	0.98	0.95	943	3	83	973	61
DUP	101 - 500	0.63	1.0	0.77	74	0	43	35	2
DUP	> 500	0.92	0.98	0.95	490	1	43	1184	48

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.9	4502	498	74	7
INDEL	1 - 100	0.64	2508	1388	43	9
SV	ALL	0.82	352	78	457	19

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.9	4502	498	74	7
INDEL	1 - 100	0.64	2508	1388	43	9
TRA	TRA	0.75	77	26	35	2
INV	> 0	0.81	54	13	44	1
DEL	> 100	0.78	93	26	104	6
DUP	> 100	0.91	128	13	278	10

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.9	4502	498	74	7
INDEL	1 - 100	0.64	2508	1388	43	9
TRA	TRA	0.75	77	26	35	2
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.81	54	13	44	1
DEL	101 - 500	0.77	23	7	12	0
DEL	> 500	0.79	70	19	92	6
DUP	101 - 500	0.67	2	1	0	0
DUP	> 500	0.91	126	12	278	10

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.85	4231	769	76	4
INDEL	1 - 100	0.66	3320	1680	47	6
SV	ALL	0.84	664	122	829	52

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.85	4231	769	76	4
INDEL	1 - 100	0.66	3320	1680	47	6
TRA	TRA	0.75	115	38	54	4
INV	> 0	0.8	189	47	162	11
DEL	> 100	0.91	264	27	257	23
DUP	> 100	0.91	96	10	379	18

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.85	4231	769	76	4
INDEL	1 - 100	0.66	3320	1680	47	6
TRA	TRA	0.75	115	38	54	4
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.8	189	47	162	11
DEL	101 - 500	0.93	40	3	21	0
DEL	> 500	0.9	224	24	236	23
DUP	101 - 500	1.0	3	0	2	0
DUP	> 500	0.9	93	10	377	18

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.85	4230	770	80	3
INDEL	1 - 100	0.72	3606	1394	40	7
SV	ALL	0.87	350	51	556	32

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.85	4230	770	80	3
INDEL	1 - 100	0.72	3606	1394	40	7
TRA	TRA	0.81	79	19	37	4
INV	> 0	0.74	25	9	19	1
DEL	> 100	0.92	166	15	212	15
DUP	> 100	0.91	80	8	292	14

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.85	4230	770	80	3
INDEL	1 - 100	0.72	3606	1394	40	7
TRA	TRA	0.81	79	19	37	4
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.74	25	9	19	1
DEL	101 - 500	0.95	37	2	18	1
DEL	> 500	0.91	129	13	195	15
DUP	101 - 500	0.0	0	0	0	0
DUP	> 500	0.91	80	8	292	14

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.0	0	0	0	0
INDEL	1 - 100	0.0	0	0	0	0
SV	ALL	0.88	1544	210	1179	65

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.0	0	0	0	0
INDEL	1 - 100	0.0	0	0	0	0
TRA	TRA	0.8	305	77	130	12
INV	> 0	0.92	304	26	223	11
DEL	> 100	0.93	675	52	590	39
DUP	> 100	0.83	260	55	304	14

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.0	0	0	0	0
INDEL	1 - 100	0.0	0	0	0	0
TRA	TRA	0.8	305	77	130	12
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.92	304	26	223	11
DEL	101 - 500	0.86	155	25	70	9
DEL	> 500	0.95	520	27	524	31
DUP	101 - 500	0.62	69	42	33	2
DUP	> 500	0.94	191	13	272	12

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.97	0.92	0.94	11553	1051	407	85	4
INDEL	1 - 100	0.83	0.91	0.86	1151	120	244	13	2
SV	ALL	0.97	0.92	0.95	234	20	7	142	16

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.97	0.92	0.94	11553	1051	407	85	4
INDEL	1 - 100	0.83	0.91	0.86	1151	120	244	13	2
TRA	TRA	1.0	0.87	0.93	45	7	0	20	2
INV	> 0	0.99	0.99	0.99	70	1	1	40	6
DEL	> 100	0.94	0.87	0.9	78	12	5	50	4
DUP	> 100	0.98	1.0	0.99	41	0	1	35	5

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.97	0.92	0.94	11553	1051	407	85	4
INDEL	1 - 100	0.83	0.91	0.86	1151	120	244	13	2
TRA	TRA	1.0	0.87	0.93	45	7	0	20	2
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	1.0	1.0	1.0	14	0	0	7	3
INV	> 500	0.98	0.98	0.98	56	1	1	33	3
DEL	101 - 500	0.79	0.55	0.65	11	9	3	3	0
DEL	> 500	0.97	0.96	0.96	67	3	2	47	4
DUP	101 - 500	1.0	1.0	1.0	12	0	0	4	0
DUP	> 500	0.97	1.0	0.98	29	0	1	31	5

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.96	0.94	0.95	11524	747	463	84	4
INDEL	1 - 100	0.81	0.92	0.86	1128	104	269	13	2
SV	ALL	0.96	0.93	0.94	229	17	10	283	16

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.96	0.94	0.95	11524	747	463	84	4
INDEL	1 - 100	0.81	0.92	0.86	1128	104	269	13	2
TRA	TRA	1.0	0.9	0.95	43	5	0	17	1
INV	> 0	0.97	0.98	0.98	63	1	2	36	7
DEL	> 100	0.97	0.89	0.93	83	10	3	59	3
DUP	> 100	0.89	0.98	0.93	40	1	5	172	6

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.96	0.94	0.95	11524	747	463	84	4
INDEL	1 - 100	0.81	0.92	0.86	1128	104	269	13	2
TRA	TRA	1.0	0.9	0.95	43	5	0	17	1
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	1.0	1.0	1.0	11	0	0	5	3
INV	> 500	0.96	0.98	0.97	52	1	2	31	4
DEL	101 - 500	0.82	0.47	0.6	9	10	2	2	0
DEL	> 500	0.99	1.0	0.99	74	0	1	57	3
DUP	101 - 500	0.71	1.0	0.83	10	0	4	5	1
DUP	> 500	0.97	0.97	0.97	30	1	1	167	5

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.7	1.0	0.82	10510	97	4490	190	10
INDEL	1 - 100	0.69	0.96	0.81	9617	83	4279	116	16
SV	ALL	0.86	1.0	0.92	2908	2	463	2651	136

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.7	1.0	0.82	10510	97	4490	190	10
INDEL	1 - 100	0.69	0.96	0.81	9617	83	4279	116	16
TRA	TRA	0.78	0.99	0.87	574	1	162	242	21
INV	> 0	0.86	1.0	0.92	571	0	96	435	21
DEL	> 100	0.89	1.0	0.94	1174	0	144	1047	67
DUP	> 100	0.91	0.99	0.94	589	1	61	1173	48

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.7	1.0	0.82	10510	97	4490	190	10
INDEL	1 - 100	0.69	0.96	0.81	9617	83	4279	116	16
TRA	TRA	0.78	0.99	0.87	574	1	162	242	21
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	0.0	1.0	0.0	0	0	0	0	0
INV	> 500	0.86	1.0	0.92	571	0	96	435	21
DEL	101 - 500	0.8	1.0	0.89	233	0	59	110	10
DEL	> 500	0.92	1.0	0.96	941	0	85	946	60
DUP	101 - 500	0.96	1.0	0.98	112	0	5	52	2
DUP	> 500	0.89	0.98	0.94	477	1	56	1124	46

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.73	3653	1347	60	6
INDEL	1 - 100	0.65	2534	1362	42	9
SV	ALL	0.77	332	98	450	19

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.73	3653	1347	60	6
INDEL	1 - 100	0.65	2534	1362	42	9
TRA	TRA	0.76	78	25	35	2
INV	> 0	0.78	52	15	40	1
DEL	> 100	0.69	82	37	77	5
DUP	> 100	0.85	120	21	302	11

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.73	3653	1347	60	6
INDEL	1 - 100	0.65	2534	1362	42	9
TRA	TRA	0.76	78	25	35	2
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.78	52	15	40	1
DEL	101 - 500	0.5	15	15	7	0
DEL	> 500	0.75	67	22	70	5
DUP	101 - 500	0.67	2	1	0	0
DUP	> 500	0.86	118	20	302	11

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.69	3436	1564	64	3
INDEL	1 - 100	0.7	3502	1498	47	6
SV	ALL	0.81	637	149	766	48

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.69	3436	1564	64	3
INDEL	1 - 100	0.7	3502	1498	47	6
TRA	TRA	0.7	107	46	47	3
INV	> 0	0.77	182	54	159	10
DEL	> 100	0.88	256	35	248	22
DUP	> 100	0.87	92	14	332	17

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.69	3436	1564	64	3
INDEL	1 - 100	0.7	3502	1498	47	6
TRA	TRA	0.7	107	46	47	3
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.77	182	54	159	10
DEL	101 - 500	0.81	35	8	18	0
DEL	> 500	0.89	221	27	230	22
DUP	101 - 500	1.0	3	0	2	0
DUP	> 500	0.86	89	14	330	17

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.68	3421	1579	68	3
INDEL	1 - 100	0.72	3581	1419	32	6
SV	ALL	0.84	336	65	532	31

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.68	3421	1579	68	3
INDEL	1 - 100	0.72	3581	1419	32	6
TRA	TRA	0.8	78	20	38	4
INV	> 0	0.71	24	10	20	1
DEL	> 100	0.87	157	24	208	15
DUP	> 100	0.88	77	11	270	13

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.68	3421	1579	68	3
INDEL	1 - 100	0.72	3581	1419	32	6
TRA	TRA	0.8	78	20	38	4
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.71	24	10	20	1
DEL	101 - 500	0.85	33	6	16	0
DEL	> 500	0.87	124	18	192	15
DUP	101 - 500	0.0	0	0	0	0
DUP	> 500	0.88	77	11	270	13

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.0	0	0	0	0
INDEL	1 - 100	0.0	0	0	0	0
SV	ALL	0.91	1603	151	1196	65

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.0	0	0	0	0
INDEL	1 - 100	0.0	0	0	0	0
TRA	TRA	0.81	311	71	128	12
INV	> 0	0.95	313	17	229	11
DEL	> 100	0.93	679	48	594	40
DUP	> 100	0.95	300	15	314	14

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.0	0	0	0	0
INDEL	1 - 100	0.0	0	0	0	0
TRA	TRA	0.81	311	71	128	12
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.95	313	17	229	11
DEL	101 - 500	0.83	150	30	69	10
DEL	> 500	0.97	529	18	531	32
DUP	101 - 500	0.96	107	4	50	2
DUP	> 500	0.95	193	11	265	12

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.87	0.99	0.93	10415	80	1545	72	4
INDEL	1 - 100	0.77	0.96	0.85	1072	44	323	12	2
SV	ALL	0.89	1.0	0.94	214	1	27	132	13

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.87	0.99	0.93	10415	80	1545	72	4
INDEL	1 - 100	0.77	0.96	0.85	1072	44	323	12	2
TRA	TRA	0.93	1.0	0.97	42	0	3	18	1
INV	> 0	0.92	1.0	0.96	65	0	6	38	6
DEL	> 100	0.84	1.0	0.92	70	0	13	46	3
DUP	> 100	0.88	0.97	0.92	37	1	5	33	4

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.87	0.99	0.93	10415	80	1545	72	4
INDEL	1 - 100	0.77	0.96	0.85	1072	44	323	12	2
TRA	TRA	0.93	1.0	0.97	42	0	3	18	1
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	0.93	1.0	0.96	13	0	1	7	3
INV	> 500	0.91	1.0	0.95	52	0	5	31	3
DEL	101 - 500	0.69	1.0	0.82	9	0	4	1	0
DEL	> 500	0.87	1.0	0.93	61	0	9	45	3
DUP	101 - 500	0.92	1.0	0.96	11	0	1	4	0
DUP	> 500	0.87	0.96	0.91	26	1	4	29	4

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.87	1.0	0.93	10395	17	1592	71	4
INDEL	1 - 100	0.76	0.96	0.85	1068	39	329	12	2
SV	ALL	0.87	1.0	0.93	208	1	31	272	14

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.87	1.0	0.93	10395	17	1592	71	4
INDEL	1 - 100	0.76	0.96	0.85	1068	39	329	12	2
TRA	TRA	0.98	0.98	0.98	42	1	1	17	1
INV	> 0	0.88	1.0	0.93	57	0	8	32	6
DEL	> 100	0.84	1.0	0.91	72	0	14	53	2
DUP	> 100	0.82	1.0	0.9	37	0	8	171	6

Variant type	Variant size	Recall	Precision	F1 score	TP	FP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.87	1.0	0.93	10395	17	1592	71	4
INDEL	1 - 100	0.76	0.96	0.85	1068	39	329	12	2
TRA	TRA	0.98	0.98	0.98	42	1	1	17	1
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	1.0	1.0	1.0	11	0	0	5	3
INV	> 500	0.85	1.0	0.92	46	0	8	27	3
DEL	101 - 500	0.64	1.0	0.78	7	0	4	1	0
DEL	> 500	0.87	1.0	0.93	65	0	10	52	2
DUP	101 - 500	0.5	1.0	0.67	7	0	7	4	1
DUP	> 500	0.97	1.0	0.98	30	0	1	167	5

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.88	0.99	0.93	13172	254	1828	233	14
INDEL	1 - 100	0.69	0.99	0.81	9579	31	4317	129	17
SV	ALL	0.78	0.97	0.86	2640	16	731	2445	128

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.88	0.99	0.93	13172	254	1828	233	14
INDEL	1 - 100	0.69	0.99	0.81	9579	31	4317	129	17
TRA	TRA	0.68	0.99	0.81	500	1	236	215	18
INV	> 0	0.77	0.99	0.87	515	1	152	392	18
DEL	> 100	0.87	0.92	0.89	1146	14	172	1047	65
DUP	> 100	0.74	1.0	0.85	479	0	171	997	45

Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*
SNV	1	0.88	0.99	0.93	13172	254	1828	233	14
INDEL	1 - 100	0.69	0.99	0.81	9579	31	4317	129	17
TRA	TRA	0.68	0.99	0.81	500	1	236	215	18
INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0
INV	101 - 500	0.0	1.0	0.0	0	0	0	0	0
INV	> 500	0.77	0.99	0.87	515	1	152	392	18
DEL	101 - 500	0.78	0.58	0.66	227	13	65	107	9
DEL	> 500	0.9	0.99	0.94	919	1	107	949	60
DUP	101 - 500	0.21	1.0	0.35	25	0	92	10	1
DUP	> 500	0.85	1.0	0.92	454	0	79	987	44

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.92	4583	417	74	7
INDEL	1 - 100	0.66	2552	1344	47	9
SV	ALL	0.76	325	105	383	17

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.92	4583	417	74	7
INDEL	1 - 100	0.66	2552	1344	47	9
TRA	TRA	0.67	69	34	35	2
INV	> 0	0.76	51	16	38	1
DEL	> 100	0.74	88	31	103	6
DUP	> 100	0.83	117	24	211	8

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.92	4583	417	74	7
INDEL	1 - 100	0.66	2552	1344	47	9
TRA	TRA	0.67	69	34	35	2
INV	1 - 100	0.0	0	0	0	0
INV	101 - 500	0.0	0	0	0	0
INV	> 500	0.76	51	16	38	1
DEL	101 - 500	0.67	20	10	11	0
DEL	> 500	0.76	68	21	92	6
DUP	101 - 500	0.67	2	1	0	0
DUP	> 500	0.83	115	23	211	8

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.86	4322	678	79	5
INDEL	1 - 100	0.69	3467	1533	50	6
SV	ALL	0.76	594	192	721	44

Variant type	Variant size	Recall	TP	FN	Prot. genes	Cancer driver prot. genes
SNV	1	0.86	4322	678	79	5
INDEL	1 - 100	0.69	3467	1533	50	6
TRA	TRA	0.58	88	65	39	2
INV	> 0	0.67	159	77	136	8
DEL	> 100	0.89	259	32	244	21
DUP	> 100	0.83	88	18	319	15

Improvement

Listing of the improvement possibilities based on the assessment results obtained from the pipelines: center_a, center_b, center_c. Browse through the improvement possibilities of the different pipelines using the tabs below.

The different combinations are described using the _and_and_or_symbols. baseline refers to the pipeline without any modification._and_refers to the intersection of two different outputs (you may use ONCOLINER's VCF intersection tool). For example, baseline_and_variant_caller_1 represents the output of the intersection of the results of the pipeline and variant caller 1._or_refers to the union of two different outputs (you may use ONCOLINER's VCF union tool). For example, variant_caller_1_or_variant_caller_2 represents the output of the union of the results of variant caller 1 and variant caller 2.

Improvement: center_a

Improvement possibilities of center_a based on its assessment results. These improvements are the result of combining the output of center_a with the outputs of different variant callers and their combinations.

(((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)_or_sage_3_0)
((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)
((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)
((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)
((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)
(cgppindel_3_9_0_or_gridss_2_13_2)
(delly_1_1_6_and_manta_1_6_0)
(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))
(gatk_4_2_6_1_and_sage_3_0)
(gridss_2_13_2_and_manta_1_6_0)
(sage_3_0_or_(strelka_2_9_10_and_svaba_1_1_0))
(sage_3_0_or_strelka_2_9_10)
delly_1_1_6
gridss_2_13_2
manta_1_6_0
sage_3_0
strelka_2_9_10
svaba_1_1_0

Use the table below to explore all improvement possibilities using the variant callers and combinations mentioned above. baseline refers to the center_a without any modification. Overall, the following improvements have the highest F1 score:

SNV: baseline_or_(((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)_or_sage_3_0)
INDEL: baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)
SV: baseline_or_gridss_2_13_2

Performance metrics (baseline vs )

Improvement selection

Explore the improvement possibilities of center_a by selecting a variant caller or combination of variant callers from the table below. Use the dropdown below to check the improvements possibilities for specific variant types and sizes. The selected improvement will be displayed in the plot above.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DUP	> 100	0.87	0.99	0.92	564	1	86	1217	50	0
baseline_or_gridss_2_13_2	DUP	> 100	0.94	0.99	0.97	614	1	36	1261	52	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DUP	> 100	0.82	1.0	0.9	444	0	97	1060	45	3
baseline_and_delly_1_1_6	DUP	> 100	0.82	1.0	0.9	487	0	105	1130	47	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	DUP	> 100	0.96	0.97	0.96	623	3	27	1289	52	3
baseline_and_manta_1_6_0	DUP	> 100	0.86	1.0	0.92	552	0	93	1193	50	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	DUP	> 100	0.85	1.0	0.92	516	0	89	1135	47	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	DUP	> 100	0.85	1.0	0.92	480	0	86	1117	47	2
baseline_and_svaba_1_1_0	DUP	> 100	0.8	1.0	0.89	502	0	126	987	46	1
baseline_and_gridss_2_13_2	DUP	> 100	0.79	1.0	0.89	526	0	136	1159	47	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 100	0.94	0.99	0.97	614	1	36	1261	52	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	DUP	> 100	0.96	0.99	0.97	621	1	29	1275	52	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DUP	101 - 500	0.63	1.0	0.77	74	43	35	2	0
baseline_or_gridss_2_13_2	DUP	101 - 500	0.91	1.0	0.96	107	10	53	2	1
baseline_and_delly_1_1_6	DUP	101 - 500	0.29	1.0	0.45	21	51	8	1	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	DUP	101 - 500	0.93	1.0	0.96	109	8	53	2	3
baseline_and_manta_1_6_0	DUP	101 - 500	0.61	1.0	0.75	69	45	34	2	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	DUP	101 - 500	0.53	1.0	0.69	50	44	24	2	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	DUP	101 - 500	0.32	1.0	0.48	20	43	8	1	2
baseline_and_svaba_1_1_0	DUP	101 - 500	0.46	1.0	0.63	62	72	30	2	1
baseline_and_gridss_2_13_2	DUP	101 - 500	0.42	1.0	0.59	54	76	26	2	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	101 - 500	0.91	1.0	0.96	107	10	53	2	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	DUP	101 - 500	0.91	1.0	0.96	107	10	53	2	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DUP	> 500	0.92	0.98	0.95	490	1	43	1184	48	0
baseline_or_gridss_2_13_2	DUP	> 500	0.95	0.98	0.97	507	1	26	1212	50	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DUP	> 500	0.89	1.0	0.94	444	0	54	1060	45	3
baseline_and_delly_1_1_6	DUP	> 500	0.9	1.0	0.95	466	0	54	1123	46	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	DUP	> 500	0.96	0.95	0.96	514	3	19	1240	50	3
baseline_and_manta_1_6_0	DUP	> 500	0.91	1.0	0.95	483	0	48	1162	48	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	DUP	> 500	0.91	1.0	0.95	466	0	45	1114	45	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	DUP	> 500	0.91	1.0	0.96	460	0	43	1110	46	2
baseline_and_svaba_1_1_0	DUP	> 500	0.89	1.0	0.94	440	0	54	959	44	1
baseline_and_gridss_2_13_2	DUP	> 500	0.89	1.0	0.94	472	0	60	1136	45	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 500	0.95	0.98	0.97	507	1	26	1212	50	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	DUP	> 500	0.96	0.98	0.97	514	1	19	1226	50	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DEL	> 100	0.91	0.88	0.89	1198	22	120	1086	68	0
baseline_or_gridss_2_13_2	DEL	> 100	0.94	0.87	0.9	1242	24	76	1113	69	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DEL	> 100	0.87	1.0	0.93	950	0	142	941	65	3
baseline_and_delly_1_1_6	DEL	> 100	0.87	0.97	0.92	1134	5	167	1041	64	1
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	DEL	> 100	0.91	0.87	0.89	1203	25	115	1086	68	3
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	DEL	> 100	0.96	0.72	0.82	1263	64	56	1138	69	3
baseline_and_manta_1_6_0	DEL	> 100	0.9	0.91	0.91	1187	16	128	1081	68	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	DEL	> 100	0.9	0.99	0.94	1054	1	122	1015	66	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	DEL	> 100	0.9	0.97	0.93	1127	5	123	1037	64	2
baseline_and_svaba_1_1_0	DEL	> 100	0.87	0.94	0.91	1083	9	163	1006	65	1
baseline_and_gridss_2_13_2	DEL	> 100	0.87	0.99	0.93	1065	1	164	1020	66	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 100	0.95	0.73	0.82	1248	60	70	1114	69	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	DEL	> 100	0.95	0.87	0.91	1252	24	66	1134	69	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DEL	101 - 500	0.87	0.51	0.65	255	19	37	121	10	0
baseline_or_gridss_2_13_2	DEL	101 - 500	0.9	0.5	0.64	263	20	29	126	11	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DEL	101 - 500	0.75	1.0	0.86	119	0	40	53	6	3
baseline_and_delly_1_1_6	DEL	101 - 500	0.82	0.79	0.81	233	5	50	110	9	1
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	DEL	101 - 500	0.89	0.48	0.62	260	22	32	123	10	3
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	DEL	101 - 500	0.93	0.33	0.49	272	40	20	129	11	3
baseline_and_manta_1_6_0	DEL	101 - 500	0.86	0.59	0.7	252	14	40	120	10	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	DEL	101 - 500	0.82	0.95	0.88	167	1	37	76	7	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	DEL	101 - 500	0.86	0.79	0.82	231	5	38	110	9	2
baseline_and_svaba_1_1_0	DEL	101 - 500	0.83	0.68	0.75	223	9	47	106	9	1
baseline_and_gridss_2_13_2	DEL	101 - 500	0.79	0.95	0.86	170	1	45	77	7	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	101 - 500	0.92	0.3	0.46	269	46	23	128	11	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	DEL	101 - 500	0.9	0.5	0.64	263	20	29	126	11	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DEL	> 500	0.92	0.98	0.95	943	3	83	973	61	0
baseline_or_gridss_2_13_2	DEL	> 500	0.95	0.97	0.96	979	4	47	997	62	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DEL	> 500	0.89	1.0	0.94	831	0	102	891	60	3
baseline_and_delly_1_1_6	DEL	> 500	0.89	1.0	0.94	901	0	117	938	58	1
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	DEL	> 500	0.92	0.98	0.95	943	3	83	973	61	3
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	DEL	> 500	0.96	0.86	0.91	991	24	36	1019	62	3
baseline_and_manta_1_6_0	DEL	> 500	0.91	0.99	0.95	935	2	88	969	61	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	DEL	> 500	0.91	1.0	0.95	887	0	85	944	61	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	DEL	> 500	0.91	1.0	0.95	896	0	85	934	58	2
baseline_and_svaba_1_1_0	DEL	> 500	0.88	1.0	0.94	860	0	116	907	59	1
baseline_and_gridss_2_13_2	DEL	> 500	0.88	1.0	0.94	895	0	119	948	61	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 500	0.95	0.91	0.93	979	14	47	997	62	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	DEL	> 500	0.96	0.97	0.97	989	4	37	1018	62	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	TRA	TRA	0.78	0.88	0.83	576	12	160	250	22	0
baseline_or_gridss_2_13_2	TRA	TRA	0.85	0.88	0.86	622	12	114	263	22	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	TRA	TRA	0.73	1.0	0.84	495	0	185	217	21	3
baseline_and_delly_1_1_6	TRA	TRA	0.72	1.0	0.84	506	0	193	223	22	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	TRA	TRA	0.89	0.72	0.8	655	34	81	277	22	3
baseline_and_manta_1_6_0	TRA	TRA	0.75	0.92	0.82	565	8	192	247	22	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	TRA	TRA	0.76	1.0	0.86	526	0	165	230	22	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	TRA	TRA	0.75	1.0	0.86	504	0	169	222	22	2
baseline_and_svaba_1_1_0	TRA	TRA	0.71	1.0	0.83	462	0	185	200	18	1
baseline_and_gridss_2_13_2	TRA	TRA	0.72	1.0	0.84	530	0	206	231	22	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	TRA	TRA	0.85	0.88	0.86	622	12	114	263	22	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	TRA	TRA	0.86	0.87	0.87	636	13	100	268	22	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	> 0	0.86	0.99	0.92	572	2	95	435	21	0
baseline_or_gridss_2_13_2	INV	> 0	0.91	0.99	0.95	606	2	61	455	21	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	INV	> 0	0.82	1.0	0.9	485	0	106	376	19	3
baseline_and_delly_1_1_6	INV	> 0	0.81	1.0	0.89	515	0	124	410	18	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	INV	> 0	0.93	0.47	0.62	622	156	45	465	21	3
baseline_and_manta_1_6_0	INV	> 0	0.85	0.99	0.91	562	2	101	426	21	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	INV	> 0	0.84	1.0	0.92	535	0	99	410	21	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	INV	> 0	0.84	1.0	0.91	509	0	97	402	18	2
baseline_and_svaba_1_1_0	INV	> 0	0.8	1.0	0.89	470	0	116	359	16	1
baseline_and_gridss_2_13_2	INV	> 0	0.81	1.0	0.89	544	0	129	419	21	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 0	0.91	0.99	0.95	606	2	61	455	21	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	INV	> 0	0.93	0.99	0.95	618	2	50	461	21	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0	0

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Precision*	FP	Prot. genes*	Added callers
baseline	INV	101 - 500	1.0	0	0	0
baseline_or_gridss_2_13_2	INV	101 - 500	1.0	0	1	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	INV	101 - 500	1.0	0	1	3
baseline_and_delly_1_1_6	INV	101 - 500	1.0	0	1	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	INV	101 - 500	0.47	28	1	3
baseline_and_manta_1_6_0	INV	101 - 500	1.0	0	1	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	INV	101 - 500	1.0	0	1	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	INV	101 - 500	1.0	0	1	2
baseline_and_svaba_1_1_0	INV	101 - 500	1.0	0	1	1
baseline_and_gridss_2_13_2	INV	101 - 500	1.0	0	1	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	101 - 500	1.0	0	1	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	INV	101 - 500	1.0	0	1	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	> 500	0.86	0.98	0.92	572	2	95	435	21	0
baseline_or_gridss_2_13_2	INV	> 500	0.91	0.98	0.94	606	2	61	455	21	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	INV	> 500	0.82	1.0	0.9	485	0	106	376	19	3
baseline_and_delly_1_1_6	INV	> 500	0.81	1.0	0.89	515	0	124	410	18	1
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	INV	> 500	0.93	0.46	0.62	622	128	45	465	21	3
baseline_and_manta_1_6_0	INV	> 500	0.85	0.98	0.91	562	2	101	426	21	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	INV	> 500	0.84	1.0	0.92	535	0	99	410	21	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	INV	> 500	0.84	1.0	0.91	509	0	97	402	18	2
baseline_and_svaba_1_1_0	INV	> 500	0.8	1.0	0.89	470	0	116	359	16	1
baseline_and_gridss_2_13_2	INV	> 500	0.81	1.0	0.89	544	0	129	419	21	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 500	0.91	0.98	0.94	606	2	61	455	21	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	INV	> 500	0.93	0.98	0.95	618	2	50	461	21	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	SV	ALL	0.86	0.93	0.89	2910	37	461	2744	140	0
baseline_or_gridss_2_13_2	SV	ALL	0.91	0.92	0.92	3084	39	287	2825	142	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	SV	ALL	0.82	1.0	0.9	2374	0	530	2407	132	3
baseline_and_delly_1_1_6	SV	ALL	0.82	0.99	0.9	2642	5	589	2582	132	1
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	SV	ALL	0.86	0.92	0.89	2915	40	456	2744	140	3
baseline_or_(delly_1_1_6_or_(gridss_2_13_2_or_manta_1_6_0))	SV	ALL	0.94	0.65	0.77	3163	257	209	2891	142	3
baseline_and_manta_1_6_0	SV	ALL	0.85	0.95	0.89	2866	26	514	2707	140	1
baseline_and_(gridss_2_13_2_and_manta_1_6_0)	SV	ALL	0.85	1.0	0.92	2631	1	475	2578	137	2
baseline_and_(delly_1_1_6_and_manta_1_6_0)	SV	ALL	0.85	0.99	0.91	2620	5	475	2559	132	2
baseline_and_svaba_1_1_0	SV	ALL	0.81	0.98	0.89	2517	9	590	2351	127	1
baseline_and_gridss_2_13_2	SV	ALL	0.81	1.0	0.89	2665	1	635	2614	137	1
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	SV	ALL	0.92	0.86	0.89	3090	75	281	2826	142	2
baseline_or_((brass_6_3_4_and_(delly_1_1_6_or_svaba_1_1_0))_or_gridss_2_13_2)	SV	ALL	0.93	0.92	0.92	3127	40	245	2865	142	4

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)_or_sage_3_0)	INDEL	1 - 100	0.86	0.91	0.88	11907	268	1989	141	19	4
baseline	INDEL	1 - 100	0.68	0.91	0.78	9434	224	4462	126	18	0
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	INDEL	1 - 100	0.88	0.78	0.83	12285	757	1611	148	19	3
baseline_or_(sage_3_0_or_strelka_2_9_10)	INDEL	1 - 100	0.89	0.77	0.83	12432	778	1464	144	19	2
baseline_or_strelka_2_9_10	INDEL	1 - 100	0.88	0.78	0.83	12217	753	1679	144	19	1
baseline_and_(gatk_4_2_6_1_and_sage_3_0)	INDEL	1 - 100	0.62	0.99	0.76	7463	10	4640	105	15	2
baseline_and_svaba_1_1_0	INDEL	1 - 100	0.55	0.99	0.71	7420	16	6052	103	12	1
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	INDEL	1 - 100	0.85	0.91	0.88	11845	264	2051	141	19	3
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INDEL	1 - 100	0.81	0.8	0.81	11269	643	2627	144	18	2
baseline_or_(sage_3_0_or_(strelka_2_9_10_and_svaba_1_1_0))	INDEL	1 - 100	0.84	0.91	0.88	11742	257	2154	139	19	3
baseline_or_sage_3_0	INDEL	1 - 100	0.83	0.91	0.87	11496	252	2400	139	19	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)_or_sage_3_0)	DEL	1 - 100	0.87	0.91	0.89	6517	139	983	100	16	4
baseline	DEL	1 - 100	0.73	0.92	0.81	5452	116	2048	91	16	0
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	DEL	1 - 100	0.9	0.75	0.82	6731	450	769	103	16	3
baseline_or_(sage_3_0_or_strelka_2_9_10)	DEL	1 - 100	0.9	0.75	0.82	6766	459	734	102	16	2
baseline_or_strelka_2_9_10	DEL	1 - 100	0.89	0.75	0.82	6687	448	813	102	16	1
baseline_and_(gatk_4_2_6_1_and_sage_3_0)	DEL	1 - 100	0.67	1.0	0.8	4334	5	2123	78	14	2
baseline_and_svaba_1_1_0	DEL	1 - 100	0.6	0.99	0.75	4480	7	3033	76	10	1
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	DEL	1 - 100	0.86	0.91	0.89	6483	137	1017	100	16	3
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	1 - 100	0.82	0.81	0.81	6157	325	1343	99	16	2
baseline_or_(sage_3_0_or_(strelka_2_9_10_and_svaba_1_1_0))	DEL	1 - 100	0.87	0.91	0.89	6535	131	965	100	16	3
baseline_or_sage_3_0	DEL	1 - 100	0.85	0.91	0.88	6363	128	1137	100	16	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)_or_sage_3_0)	INS/DUP	1 - 100	0.84	0.91	0.87	5390	129	1006	45	6	4
baseline	INS/DUP	1 - 100	0.62	0.9	0.74	3982	108	2414	37	4	0
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	INS/DUP	1 - 100	0.87	0.81	0.84	5554	307	842	49	6	3
baseline_or_(sage_3_0_or_strelka_2_9_10)	INS/DUP	1 - 100	0.89	0.8	0.84	5666	319	730	46	6	2
baseline_or_strelka_2_9_10	INS/DUP	1 - 100	0.86	0.81	0.84	5530	305	866	46	6	1
baseline_and_(gatk_4_2_6_1_and_sage_3_0)	INS/DUP	1 - 100	0.55	0.99	0.71	3129	5	2517	30	3	2
baseline_and_svaba_1_1_0	INS/DUP	1 - 100	0.49	0.99	0.66	2940	9	3019	28	2	1
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	INS/DUP	1 - 100	0.84	0.91	0.87	5362	127	1034	45	6	3
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INS/DUP	1 - 100	0.8	0.8	0.8	5112	318	1284	48	4	2
baseline_or_(sage_3_0_or_(strelka_2_9_10_and_svaba_1_1_0))	INS/DUP	1 - 100	0.81	0.91	0.86	5207	126	1189	43	6	3
baseline_or_sage_3_0	INS/DUP	1 - 100	0.8	0.91	0.85	5133	124	1263	43	6	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)_or_sage_3_0)	SNV	1	0.91	0.93	0.92	13645	1855	1355	241	14	4
baseline	SNV	1	0.86	0.93	0.89	12963	1798	2037	228	12	0
baseline_or_((cgppindel_3_9_0_and_svaba_1_1_0)_or_strelka_2_9_10)	SNV	1	0.93	0.88	0.9	13898	3265	1102	250	15	3
baseline_or_(sage_3_0_or_strelka_2_9_10)	SNV	1	0.94	0.88	0.91	14046	3281	954	251	15	2
baseline_or_strelka_2_9_10	SNV	1	0.93	0.88	0.9	13898	3265	1102	250	15	1
baseline_and_(gatk_4_2_6_1_and_sage_3_0)	SNV	1	0.82	1.0	0.9	10083	57	2161	186	10	2
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	SNV	1	0.89	0.93	0.91	13372	1821	1628	235	12	3
baseline_or_(sage_3_0_or_(strelka_2_9_10_and_svaba_1_1_0))	SNV	1	0.89	0.93	0.91	13372	1821	1628	235	12	3
baseline_or_sage_3_0	SNV	1	0.89	0.93	0.91	13372	1821	1628	235	12	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Improvement: center_b

Improvement possibilities of center_b based on its assessment results. These improvements are the result of combining the output of center_b with the outputs of different variant callers and their combinations.

((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)
((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)
((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))
((cgpcavemanwrapper_1_16_0_or_strelka_2_9_10)_and_gatk_4_2_6_1)
((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)
((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)
((gatk_4_2_6_1_and_strelka_2_9_10)_or_muse_2_0)
((gatk_4_2_6_1_or_svaba_1_1_0)_and_strelka_2_9_10)
(cgpcavemanwrapper_1_16_0_and_gatk_4_2_6_1)
(cgppindel_3_9_0_and_strelka_2_9_10)
(cgppindel_3_9_0_and_svaba_1_1_0)
(gatk_4_2_6_1_and_(strelka_2_9_10_or_svaba_1_1_0))
(gatk_4_2_6_1_and_strelka_2_9_10)
(gridss_2_13_2_or_manta_1_6_0)
(strelka_2_9_10_and_svaba_1_1_0)
manta_1_6_0
muse_2_0

Use the table below to explore all improvement possibilities using the variant callers and combinations mentioned above. baseline refers to the center_b without any modification. Overall, the following improvements have the highest F1 score:

SNV: baseline_or_((cgpcavemanwrapper_1_16_0_or_strelka_2_9_10)_and_gatk_4_2_6_1)
INDEL: baseline_or_((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)
SV: baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)

Performance metrics (baseline vs )

Improvement selection

Explore the improvement possibilities of center_b by selecting a variant caller or combination of variant callers from the table below. Use the dropdown below to check the improvements possibilities for specific variant types and sizes. The selected improvement will be displayed in the plot above.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DUP	> 100	0.91	0.99	0.94	589	1	61	1173	48	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	DUP	> 100	0.95	0.99	0.97	615	1	35	1218	51	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	DUP	> 100	0.95	0.98	0.96	620	2	30	1264	52	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	DUP	> 100	0.95	0.99	0.97	617	1	33	1259	52	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 100	0.96	0.98	0.97	625	2	25	1277	52	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	DUP	> 100	0.93	0.99	0.96	607	1	43	1207	51	3
baseline_or_manta_1_6_0	DUP	> 100	0.95	0.98	0.96	620	2	30	1264	52	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DUP	101 - 500	0.96	1.0	0.98	112	5	52	2	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	DUP	101 - 500	0.97	1.0	0.98	113	4	54	2	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	DUP	101 - 500	0.98	1.0	0.99	115	2	55	2	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	DUP	101 - 500	0.97	1.0	0.98	113	4	54	2	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	101 - 500	0.98	1.0	0.99	115	2	55	2	2
baseline_or_manta_1_6_0	DUP	101 - 500	0.98	1.0	0.99	115	2	55	2	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DUP	> 500	0.89	0.98	0.94	477	1	56	1124	46	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	DUP	> 500	0.94	0.98	0.96	502	1	31	1168	49	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	DUP	> 500	0.95	0.97	0.96	505	2	28	1213	50	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	DUP	> 500	0.95	0.98	0.96	504	1	29	1209	50	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 500	0.96	0.97	0.96	510	2	23	1226	50	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	DUP	> 500	0.93	0.98	0.95	495	1	38	1158	49	3
baseline_or_manta_1_6_0	DUP	> 500	0.95	0.97	0.96	505	2	28	1213	50	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	DEL	> 100	0.9	0.96	0.93	1189	6	129	1054	67	2
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	DEL	> 100	0.94	0.94	0.94	1241	10	77	1124	68	4
baseline	DEL	> 100	0.89	1.0	0.94	1174	0	144	1047	67	0
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	DEL	> 100	0.95	0.88	0.91	1250	23	68	1111	69	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	DEL	> 100	0.92	0.98	0.95	1211	3	107	1095	69	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 100	0.95	0.88	0.91	1251	23	67	1116	69	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	DEL	> 100	0.92	0.96	0.94	1213	6	105	1067	67	3
baseline_or_manta_1_6_0	DEL	> 100	0.95	0.88	0.91	1246	21	72	1110	69	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	DEL	101 - 500	0.85	0.76	0.8	247	6	45	118	11	2
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	DEL	101 - 500	0.89	0.66	0.75	260	10	32	124	11	4
baseline_or_(gatk_4_2_6_1_and_(strelka_2_9_10_or_svaba_1_1_0))	DEL	101 - 500	0.8	0.94	0.87	235	1	57	111	10	3
baseline	DEL	101 - 500	0.8	1.0	0.89	233	0	59	110	10	0
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	DEL	101 - 500	0.93	0.54	0.69	271	16	21	128	11	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	DEL	101 - 500	0.82	0.9	0.86	239	2	53	113	11	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	101 - 500	0.92	0.53	0.67	268	17	24	128	11	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	DEL	101 - 500	0.85	0.76	0.8	247	6	45	118	11	3
baseline_or_manta_1_6_0	DEL	101 - 500	0.91	0.54	0.68	267	16	25	127	11	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	DEL	> 500	0.92	1.0	0.96	942	0	84	947	60	2
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	DEL	> 500	0.96	1.0	0.98	981	0	45	1010	61	4
baseline	DEL	> 500	0.92	1.0	0.96	941	0	85	946	60	0
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	DEL	> 500	0.95	0.95	0.95	979	7	47	993	62	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	DEL	> 500	0.95	0.99	0.97	972	1	54	992	62	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 500	0.96	0.96	0.96	983	6	43	998	62	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	DEL	> 500	0.94	1.0	0.97	966	0	60	960	60	3
baseline_or_manta_1_6_0	DEL	> 500	0.95	0.97	0.96	979	5	47	993	62	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	TRA	TRA	0.78	0.99	0.87	574	1	162	242	21	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	TRA	TRA	0.83	0.98	0.9	610	2	127	255	22	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	TRA	TRA	0.88	0.79	0.83	644	24	92	274	22	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	TRA	TRA	0.81	0.99	0.89	599	1	138	252	22	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	TRA	TRA	0.88	0.79	0.83	645	24	91	274	22	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	TRA	TRA	0.81	0.99	0.89	596	1	141	250	21	3
baseline_or_manta_1_6_0	TRA	TRA	0.88	0.79	0.83	644	24	92	274	22	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	> 0	0.86	1.0	0.92	571	0	96	435	21	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	INV	> 0	0.91	1.0	0.95	606	0	61	457	21	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	INV	> 0	0.91	0.94	0.92	606	9	61	456	21	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	INV	> 0	0.89	1.0	0.94	593	0	74	449	21	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 0	0.91	0.94	0.93	609	9	58	459	21	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	INV	> 0	0.88	1.0	0.94	586	0	81	444	21	3
baseline_or_manta_1_6_0	INV	> 0	0.91	0.94	0.92	606	9	61	456	21	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0	0

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Precision*	FP	Prot. genes*	Added callers
baseline	INV	101 - 500	1.0	0	0	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	INV	101 - 500	1.0	0	1	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	INV	101 - 500	0.96	1	1	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	INV	101 - 500	1.0	0	1	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	101 - 500	0.96	1	1	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	INV	101 - 500	1.0	0	1	3
baseline_or_manta_1_6_0	INV	101 - 500	0.96	1	1	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	> 500	0.86	1.0	0.92	571	0	96	435	21	0
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	INV	> 500	0.91	1.0	0.95	606	0	61	457	21	4
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	INV	> 500	0.91	0.93	0.92	606	8	61	456	21	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	INV	> 500	0.89	1.0	0.94	593	0	74	449	21	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 500	0.91	0.93	0.92	609	8	58	459	21	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	INV	> 500	0.88	1.0	0.94	586	0	81	444	21	3
baseline_or_manta_1_6_0	INV	> 500	0.91	0.93	0.92	606	8	61	456	21	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	SV	ALL	0.87	0.98	0.92	2923	8	448	2657	136	2
baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	SV	ALL	0.91	0.97	0.94	3072	13	300	2782	140	4
baseline	SV	ALL	0.86	1.0	0.92	2908	2	463	2651	136	0
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_manta_1_6_0)	SV	ALL	0.93	0.89	0.91	3120	58	251	2830	142	3
baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	SV	ALL	0.9	0.99	0.94	3020	5	352	2793	142	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	SV	ALL	0.93	0.89	0.91	3130	58	241	2849	142	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	SV	ALL	0.89	0.98	0.93	3002	8	370	2707	138	3
baseline_or_manta_1_6_0	SV	ALL	0.92	0.89	0.91	3116	56	255	2829	142	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	INDEL	1 - 100	0.73	0.96	0.83	10180	91	3716	130	18	2
baseline	INDEL	1 - 100	0.69	0.96	0.81	9617	83	4279	116	16	0
baseline_or_(gatk_4_2_6_1_and_(strelka_2_9_10_or_svaba_1_1_0))	INDEL	1 - 100	0.8	0.96	0.87	11150	114	2746	138	18	3
baseline_or_((gatk_4_2_6_1_and_strelka_2_9_10)_or_muse_2_0)	INDEL	1 - 100	0.79	0.96	0.86	10959	111	2937	133	18	3
baseline_or_(strelka_2_9_10_and_svaba_1_1_0)	INDEL	1 - 100	0.76	0.96	0.85	10516	93	3380	127	18	2
baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	INDEL	1 - 100	0.79	0.96	0.86	10959	111	2937	133	18	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	INDEL	1 - 100	0.73	0.96	0.83	10180	91	3716	130	18	3
baseline_or_((cgpcavemanwrapper_1_16_0_or_strelka_2_9_10)_and_gatk_4_2_6_1)	INDEL	1 - 100	0.79	0.96	0.86	10959	111	2937	133	18	3
baseline_or_((gatk_4_2_6_1_or_svaba_1_1_0)_and_strelka_2_9_10)	INDEL	1 - 100	0.8	0.95	0.87	11180	117	2716	133	18	3
baseline_or_((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)	INDEL	1 - 100	0.81	0.95	0.88	11295	122	2601	135	18	3
baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	INDEL	1 - 100	0.77	0.96	0.85	10665	100	3231	130	18	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	DEL	1 - 100	0.76	0.96	0.85	5673	51	1827	92	15	2
baseline	DEL	1 - 100	0.71	0.96	0.81	5292	47	2208	85	14	0
baseline_or_(gatk_4_2_6_1_and_(strelka_2_9_10_or_svaba_1_1_0))	DEL	1 - 100	0.82	0.96	0.89	6184	56	1316	98	15	3
baseline_or_((gatk_4_2_6_1_and_strelka_2_9_10)_or_muse_2_0)	DEL	1 - 100	0.8	0.96	0.87	6034	56	1466	95	15	3
baseline_or_(strelka_2_9_10_and_svaba_1_1_0)	DEL	1 - 100	0.78	0.96	0.86	5878	53	1622	91	15	2
baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	DEL	1 - 100	0.8	0.96	0.87	6034	56	1466	95	15	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	DEL	1 - 100	0.76	0.96	0.85	5673	51	1827	92	15	3
baseline_or_((cgpcavemanwrapper_1_16_0_or_strelka_2_9_10)_and_gatk_4_2_6_1)	DEL	1 - 100	0.8	0.96	0.87	6034	56	1466	95	15	3
baseline_or_((gatk_4_2_6_1_or_svaba_1_1_0)_and_strelka_2_9_10)	DEL	1 - 100	0.83	0.95	0.89	6191	60	1309	95	15	3
baseline_or_((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)	DEL	1 - 100	0.82	0.95	0.88	6148	65	1352	95	15	3
baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	DEL	1 - 100	0.77	0.95	0.85	5786	57	1714	92	15	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	INS/DUP	1 - 100	0.7	0.96	0.81	4507	40	1889	42	6	2
baseline	INS/DUP	1 - 100	0.68	0.97	0.8	4325	36	2071	34	5	0
baseline_or_(gatk_4_2_6_1_and_(strelka_2_9_10_or_svaba_1_1_0))	INS/DUP	1 - 100	0.78	0.95	0.86	4966	58	1430	44	6	3
baseline_or_((gatk_4_2_6_1_and_strelka_2_9_10)_or_muse_2_0)	INS/DUP	1 - 100	0.77	0.95	0.85	4925	55	1471	42	6	3
baseline_or_(strelka_2_9_10_and_svaba_1_1_0)	INS/DUP	1 - 100	0.73	0.96	0.83	4638	40	1758	40	6	2
baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	INS/DUP	1 - 100	0.77	0.95	0.85	4925	55	1471	42	6	2
baseline_or_((brass_6_3_4_or_cgppindel_3_9_0)_and_svaba_1_1_0)	INS/DUP	1 - 100	0.7	0.96	0.81	4507	40	1889	42	6	3
baseline_or_((cgpcavemanwrapper_1_16_0_or_strelka_2_9_10)_and_gatk_4_2_6_1)	INS/DUP	1 - 100	0.77	0.95	0.85	4925	55	1471	42	6	3
baseline_or_((gatk_4_2_6_1_or_svaba_1_1_0)_and_strelka_2_9_10)	INS/DUP	1 - 100	0.78	0.95	0.86	4989	57	1407	42	6	3
baseline_or_((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)	INS/DUP	1 - 100	0.8	0.96	0.87	5147	57	1249	44	6	3
baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	INS/DUP	1 - 100	0.76	0.97	0.85	4879	43	1517	42	6	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	SNV	1	0.7	1.0	0.82	10510	97	4490	190	10	0
baseline_or_(gatk_4_2_6_1_and_(strelka_2_9_10_or_svaba_1_1_0))	SNV	1	0.88	0.98	0.93	13170	456	1830	234	14	3
baseline_or_muse_2_0	SNV	1	0.84	0.96	0.9	12594	904	2406	224	12	1
baseline_or_((gatk_4_2_6_1_and_strelka_2_9_10)_or_muse_2_0)	SNV	1	0.92	0.95	0.93	13738	1196	1262	241	14	3
baseline_or_(cgpcavemanwrapper_1_16_0_and_gatk_4_2_6_1)	SNV	1	0.87	0.99	0.92	13001	224	1999	235	14	2
baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	SNV	1	0.88	0.98	0.93	13170	456	1830	234	14	2
baseline_or_((cgpcavemanwrapper_1_16_0_or_strelka_2_9_10)_and_gatk_4_2_6_1)	SNV	1	0.9	0.98	0.94	13470	486	1530	237	14	3
baseline_or_((gatk_4_2_6_1_or_svaba_1_1_0)_and_strelka_2_9_10)	SNV	1	0.88	0.98	0.93	13170	456	1830	234	14	3
baseline_or_((cgppindel_3_9_0_or_gatk_4_2_6_1)_and_strelka_2_9_10)	SNV	1	0.88	0.98	0.93	13170	456	1830	234	14	3

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Improvement: center_c

Improvement possibilities of center_c based on its assessment results. These improvements are the result of combining the output of center_c with the outputs of different variant callers and their combinations.

((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)
((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)
((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)
((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))
((cgppindel_3_9_0_or_sage_3_0)_and_strelka_2_9_10)
(cgppindel_3_9_0_and_strelka_2_9_10)
(cgppindel_3_9_0_or_gridss_2_13_2)
(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))
(gridss_2_13_2_and_svaba_1_1_0)
(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))
(gridss_2_13_2_or_manta_1_6_0)
(manta_1_6_0_and_svaba_1_1_0)
(muse_2_0_or_sage_3_0)
gridss_2_13_2
manta_1_6_0
sage_3_0

Use the table below to explore all improvement possibilities using the variant callers and combinations mentioned above. baseline refers to the center_c without any modification. Overall, the following improvements have the highest F1 score:

SNV: baseline_or_sage_3_0
INDEL: baseline_or_((cgppindel_3_9_0_or_sage_3_0)_and_strelka_2_9_10)
SV: baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))

Performance metrics (baseline vs )

Improvement selection

Explore the improvement possibilities of center_c by selecting a variant caller or combination of variant callers from the table below. Use the dropdown below to check the improvements possibilities for specific variant types and sizes. The selected improvement will be displayed in the plot above.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 100	0.72	1.0	0.84	448	0	171	963	44	3
baseline_or_gridss_2_13_2	DUP	> 100	0.91	1.0	0.95	589	0	61	1248	51	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DUP	> 100	0.68	1.0	0.81	425	0	201	936	42	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	DUP	> 100	0.67	1.0	0.8	449	0	219	963	44	2
baseline	DUP	> 100	0.74	1.0	0.85	479	0	171	997	45	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 100	0.93	1.0	0.96	603	0	47	1257	52	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 100	0.95	0.99	0.97	619	1	31	1280	52	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 100	0.91	1.0	0.95	589	0	61	1248	51	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	DUP	> 100	0.91	1.0	0.95	589	0	61	1248	51	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DUP	> 100	0.72	1.0	0.84	449	0	171	927	42	4
baseline_or_manta_1_6_0	DUP	> 100	0.88	0.99	0.93	573	1	77	1228	52	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	> 100	0.66	1.0	0.8	450	0	227	927	42	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DUP	101 - 500	0.16	1.0	0.28	18	92	8	1	3
baseline_or_gridss_2_13_2	DUP	101 - 500	0.77	1.0	0.87	90	27	44	2	1
baseline	DUP	101 - 500	0.21	1.0	0.35	25	92	10	1	0
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	DUP	101 - 500	0.12	1.0	0.22	18	131	8	1	2
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DUP	101 - 500	0.87	1.0	0.93	102	15	52	2	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	101 - 500	0.92	1.0	0.96	108	9	53	2	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	101 - 500	0.77	1.0	0.87	90	27	44	2	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	DUP	101 - 500	0.77	1.0	0.87	90	27	44	2	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DUP	101 - 500	0.19	1.0	0.32	22	92	10	1	4
baseline_or_manta_1_6_0	DUP	101 - 500	0.67	1.0	0.8	78	39	37	2	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	101 - 500	0.14	1.0	0.24	22	140	10	1	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 500	0.84	1.0	0.92	430	0	79	956	43	3
baseline_or_gridss_2_13_2	DUP	> 500	0.94	1.0	0.97	499	0	34	1208	49	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DUP	> 500	0.8	1.0	0.89	425	0	109	936	42	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	DUP	> 500	0.83	1.0	0.91	431	0	88	956	43	2
baseline	DUP	> 500	0.85	1.0	0.92	454	0	79	987	44	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 500	0.94	1.0	0.97	501	0	32	1209	50	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 500	0.96	0.98	0.97	511	1	22	1231	50	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 500	0.94	1.0	0.97	499	0	34	1208	49	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	DUP	> 500	0.94	1.0	0.97	499	0	34	1208	49	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DUP	> 500	0.84	1.0	0.92	427	0	79	918	41	4
baseline_or_manta_1_6_0	DUP	> 500	0.93	0.98	0.96	495	1	38	1194	50	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	> 500	0.83	1.0	0.91	428	0	87	918	41	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 100	0.86	0.97	0.91	1043	4	174	985	62	3
baseline_or_gridss_2_13_2	DEL	> 100	0.93	0.91	0.92	1222	16	96	1104	68	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DEL	> 100	0.82	1.0	0.9	938	0	206	913	63	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	DEL	> 100	0.84	0.97	0.9	1058	5	196	993	63	2
baseline	DEL	> 100	0.87	0.92	0.89	1146	14	172	1047	65	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 100	0.94	0.89	0.91	1234	20	85	1110	69	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 100	0.95	0.83	0.89	1257	32	62	1120	69	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 100	0.93	0.77	0.84	1230	49	88	1109	68	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	DEL	> 100	0.93	0.9	0.92	1228	18	90	1107	68	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DEL	> 100	0.86	0.98	0.91	1030	3	174	974	61	4
baseline_or_manta_1_6_0	DEL	> 100	0.94	0.84	0.89	1234	30	85	1102	69	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	> 100	0.84	0.99	0.91	982	1	191	955	63	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	101 - 500	0.76	0.81	0.79	209	4	65	99	8	3
baseline_or_gridss_2_13_2	DEL	101 - 500	0.87	0.58	0.69	253	14	39	118	10	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DEL	101 - 500	0.62	1.0	0.77	116	0	71	51	6	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	DEL	101 - 500	0.75	0.78	0.77	214	5	72	101	8	2
baseline	DEL	101 - 500	0.78	0.58	0.66	227	13	65	107	9	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DEL	101 - 500	0.88	0.51	0.65	257	18	35	121	11	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	101 - 500	0.92	0.43	0.59	270	25	22	128	11	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	101 - 500	0.89	0.34	0.49	261	37	31	123	10	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	DEL	101 - 500	0.89	0.58	0.7	259	14	33	121	10	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DEL	101 - 500	0.76	0.85	0.8	203	3	65	96	7	4
baseline_or_manta_1_6_0	DEL	101 - 500	0.9	0.44	0.59	264	24	28	125	11	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	101 - 500	0.68	0.94	0.79	149	1	69	69	6	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 500	0.88	1.0	0.94	834	0	109	892	57	3
baseline_or_gridss_2_13_2	DEL	> 500	0.94	0.99	0.96	969	2	57	997	62	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	DEL	> 500	0.86	1.0	0.92	822	0	135	867	59	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	DEL	> 500	0.87	1.0	0.93	844	0	124	899	58	2
baseline	DEL	> 500	0.9	0.99	0.94	919	1	107	949	60	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 500	0.95	0.99	0.97	977	2	50	1000	62	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 500	0.96	0.95	0.96	987	7	40	1003	62	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 500	0.94	0.92	0.93	969	12	57	997	62	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	DEL	> 500	0.94	0.97	0.96	969	4	57	997	62	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DEL	> 500	0.88	1.0	0.94	827	0	109	884	57	4
baseline_or_manta_1_6_0	DEL	> 500	0.94	0.96	0.95	970	6	57	988	62	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	> 500	0.87	1.0	0.93	833	0	122	890	59	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	TRA	TRA	0.65	1.0	0.79	447	0	237	195	18	3
baseline_or_gridss_2_13_2	TRA	TRA	0.8	0.99	0.89	591	1	145	249	22	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	TRA	TRA	0.63	1.0	0.77	478	0	278	208	18	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	TRA	TRA	0.64	1.0	0.78	452	0	249	197	18	2
baseline	TRA	TRA	0.68	0.99	0.81	500	1	236	215	18	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	TRA	TRA	0.8	0.99	0.89	593	1	144	250	22	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	TRA	TRA	0.88	0.79	0.83	644	24	92	274	22	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	TRA	TRA	0.8	0.99	0.89	591	1	145	249	22	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	TRA	TRA	0.8	0.99	0.89	591	1	145	249	22	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	TRA	TRA	0.65	1.0	0.79	446	0	237	194	18	4
baseline_or_manta_1_6_0	TRA	TRA	0.84	0.79	0.81	615	24	121	265	22	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	TRA	TRA	0.64	1.0	0.78	452	0	252	196	18	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	INV	> 0	0.74	1.0	0.85	437	0	152	343	14	3
baseline_or_gridss_2_13_2	INV	> 0	0.89	0.99	0.94	596	1	71	453	21	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	INV	> 0	0.7	1.0	0.83	455	0	193	353	17	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	INV	> 0	0.74	1.0	0.85	458	0	161	352	15	2
baseline	INV	> 0	0.77	0.99	0.87	515	1	152	392	18	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	INV	> 0	0.9	0.99	0.94	599	1	68	454	21	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 0	0.92	0.93	0.93	614	10	53	461	21	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 0	0.89	0.99	0.94	596	1	71	453	21	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	INV	> 0	0.89	0.99	0.94	596	1	71	453	21	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	INV	> 0	0.74	1.0	0.85	436	0	153	341	14	4
baseline_or_manta_1_6_0	INV	> 0	0.89	0.93	0.91	591	10	76	446	21	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	> 0	0.74	1.0	0.85	461	0	160	350	15	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INV	1 - 100	0.0	0.0	0.0	0	0	0	0	0	0

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Precision*	FP	Prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	INV	101 - 500	1.0	0	1	3
baseline_or_gridss_2_13_2	INV	101 - 500	1.0	0	1	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	INV	101 - 500	1.0	0	1	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	INV	101 - 500	1.0	0	1	2
baseline	INV	101 - 500	1.0	0	0	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	INV	101 - 500	1.0	0	1	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	101 - 500	0.96	1	1	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	101 - 500	1.0	0	1	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	INV	101 - 500	1.0	0	1	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	INV	101 - 500	1.0	0	1	4
baseline_or_manta_1_6_0	INV	101 - 500	0.96	1	1	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	101 - 500	1.0	0	1	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	INV	> 500	0.74	1.0	0.85	437	0	152	343	14	3
baseline_or_gridss_2_13_2	INV	> 500	0.89	0.99	0.94	596	1	71	453	21	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	INV	> 500	0.7	1.0	0.83	455	0	193	353	17	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	INV	> 500	0.74	1.0	0.85	458	0	161	352	15	2
baseline	INV	> 500	0.77	0.99	0.87	515	1	152	392	18	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	INV	> 500	0.9	0.99	0.94	599	1	68	454	21	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 500	0.92	0.92	0.92	614	9	53	461	21	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 500	0.89	0.99	0.94	596	1	71	453	21	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	INV	> 500	0.89	0.99	0.94	596	1	71	453	21	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	INV	> 500	0.74	1.0	0.85	436	0	153	341	14	4
baseline_or_manta_1_6_0	INV	> 500	0.89	0.92	0.91	591	9	76	446	21	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	> 500	0.74	1.0	0.85	461	0	160	350	15	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	SV	ALL	0.76	0.99	0.86	2375	4	734	2296	122	3
baseline_or_gridss_2_13_2	SV	ALL	0.89	0.96	0.92	2998	18	373	2800	141	1
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	SV	ALL	0.72	1.0	0.84	2296	0	878	2236	123	3
baseline_and_(manta_1_6_0_and_svaba_1_1_0)	SV	ALL	0.75	0.99	0.85	2417	5	825	2314	124	2
baseline	SV	ALL	0.78	0.97	0.86	2640	16	731	2445	128	0
baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	SV	ALL	0.9	0.95	0.93	3029	22	344	2808	142	3
baseline_or_(gridss_2_13_2_or_manta_1_6_0)	SV	ALL	0.93	0.87	0.9	3134	67	238	2859	142	2
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	SV	ALL	0.89	0.9	0.9	3006	51	365	2803	141	2
baseline_or_((cgppindel_3_9_0_and_delly_1_1_6)_or_gridss_2_13_2)	SV	ALL	0.89	0.96	0.92	3004	20	367	2801	141	3
baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	SV	ALL	0.76	0.99	0.86	2361	3	735	2253	120	4
baseline_or_manta_1_6_0	SV	ALL	0.89	0.88	0.89	3013	65	359	2783	142	1
baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	SV	ALL	0.74	1.0	0.85	2345	1	830	2246	122	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INDEL	1 - 100	0.69	0.99	0.81	9579	31	4317	129	17	0
baseline_or_((cgppindel_3_9_0_or_sage_3_0)_and_strelka_2_9_10)	INDEL	1 - 100	0.79	0.98	0.88	11028	44	2868	140	18	3
baseline_or_(muse_2_0_or_sage_3_0)	INDEL	1 - 100	0.79	0.98	0.87	10999	60	2897	138	18	2
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	INDEL	1 - 100	0.81	0.97	0.88	11270	70	2626	140	18	3
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INDEL	1 - 100	0.75	0.85	0.8	10440	443	3456	138	17	2
baseline_or_sage_3_0	INDEL	1 - 100	0.79	0.98	0.87	10999	60	2897	138	18	1
baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	INDEL	1 - 100	0.74	0.98	0.84	10272	43	3624	136	17	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	DEL	1 - 100	0.74	0.99	0.85	5553	14	1947	93	15	0
baseline_or_((cgppindel_3_9_0_or_sage_3_0)_and_strelka_2_9_10)	DEL	1 - 100	0.81	0.98	0.89	6079	23	1421	98	15	3
baseline_or_(muse_2_0_or_sage_3_0)	DEL	1 - 100	0.81	0.98	0.89	6102	26	1398	98	15	2
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	DEL	1 - 100	0.82	0.97	0.89	6176	34	1324	98	15	3
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	1 - 100	0.76	0.85	0.81	5724	219	1776	96	15	2
baseline_or_sage_3_0	DEL	1 - 100	0.81	0.98	0.89	6102	26	1398	98	15	1
baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	DEL	1 - 100	0.76	0.98	0.86	5693	23	1807	96	15	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	INS/DUP	1 - 100	0.63	0.98	0.77	4026	17	2370	38	4	0
baseline_or_((cgppindel_3_9_0_or_sage_3_0)_and_strelka_2_9_10)	INS/DUP	1 - 100	0.77	0.98	0.87	4949	21	1447	46	6	3
baseline_or_(muse_2_0_or_sage_3_0)	INS/DUP	1 - 100	0.77	0.97	0.86	4897	34	1499	44	6	2
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	INS/DUP	1 - 100	0.8	0.97	0.88	5094	36	1302	46	6	3
baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INS/DUP	1 - 100	0.74	0.85	0.79	4716	224	1680	45	4	2
baseline_or_sage_3_0	INS/DUP	1 - 100	0.77	0.97	0.86	4897	34	1499	44	6	1
baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	INS/DUP	1 - 100	0.72	0.98	0.83	4579	20	1817	43	4	2

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Operation	Variant type	Variant size	Recall*	Precision*	F1 score*	TP	FP	FN	Prot. genes*	Cancer driver prot. genes*	Added callers
baseline	SNV	1	0.88	0.99	0.93	13172	254	1828	233	14	0
baseline_or_((cgppindel_3_9_0_or_sage_3_0)_and_strelka_2_9_10)	SNV	1	0.89	0.99	0.93	13295	260	1705	237	14	3
baseline_or_(muse_2_0_or_sage_3_0)	SNV	1	0.9	0.96	0.93	13575	976	1425	241	14	2
baseline_or_((cgppindel_3_9_0_and_strelka_2_9_10)_or_sage_3_0)	SNV	1	0.89	0.99	0.94	13408	276	1592	238	14	3
baseline_or_sage_3_0	SNV	1	0.89	0.99	0.94	13408	276	1592	238	14	1

*Recall: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*F1 score: F1-score is calculated using the precision and recall values from the precision and recall samples respectively.

*Prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes: Warning: ONCOLINER does not compute genes linked to false positives.

Harmonization

Listing of the harmonization options based on the improvement possibilities of the pipelines: center_a, center_b, center_c.

Use the table below to explore all harmonization options. Overall, the following combinations have the lowest heterogeneity score (PHS):

SNV:

center_a: baseline_or_sage_3_0
center_b: baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)
center_c: baseline_or_sage_3_0

INDEL:

center_a: baseline_or_sage_3_0
center_b: baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)
center_c: baseline_or_sage_3_0

center_a: baseline_or_gridss_2_13_2
center_b: baseline_or_manta_1_6_0
center_c: baseline_or_(gridss_2_13_2_or_manta_1_6_0)

Performance metrics (baseline vs harmonization)

Harmonization selection

Explore the harmonization options by selecting any row from the table below. Use the dropdown below to check the harmonization options for specific variant types and sizes. The selected harmonization will be displayed in the plot above.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	INV	> 0	0.03	0.87	0.99	0.93	0.09	441.0	21.0	1
baseline	baseline	baseline	INV	> 0	0.05	0.83	0.99	0.9	0.18	420.67	20.0	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 0	0.03	0.87	0.99	0.93	0.09	441.0	21.0	2
baseline	baseline	baseline_or_manta_1_6_0	INV	> 0	0.04	0.87	0.97	0.92	0.1	438.67	21.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	INV	> 0	0.04	0.89	0.97	0.93	0.07	448.0	21.0	2
baseline	baseline_or_manta_1_6_0	baseline	INV	> 0	0.08	0.85	0.97	0.9	0.16	427.67	20.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	INV	> 0	0.05	0.89	0.97	0.93	0.07	448.33	21.0	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	INV	> 0	0.04	0.88	0.95	0.92	0.05	445.67	21.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	INV	> 0	0.03	0.89	0.99	0.94	0.06	447.67	21.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 0	0.05	0.9	0.97	0.93	0.06	450.33	21.0	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 0	0.03	0.89	0.99	0.94	0.06	447.67	21.0	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	INV	> 0	0.01	0.9	0.99	0.95	0.03	455.0	21.0	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	INV	> 0	0.01	0.9	0.99	0.94	0.03	452.33	21.0	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	INV	> 0	0.03	0.91	0.97	0.94	0.03	455.67	21.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	INV	> 0	0.03	0.9	0.97	0.94	0.03	454.67	21.0	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 0	0.03	0.91	0.95	0.93	0.02	457.33	21.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	INV	> 0	0.04	0.9	0.95	0.93	0.05	452.33	21.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	> 0	0.06	0.81	1.0	0.89	0.26	387.0	18.33	5
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	INV	> 0	0.04	0.85	1.0	0.92	0.13	432.67	20.0	2
baseline_and_delly_1_1_6	baseline	baseline	INV	> 0	0.04	0.81	1.0	0.89	0.19	412.33	19.0	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	INV	> 0	0.03	0.87	0.99	0.92	0.11	438.0	21.0	2
baseline_and_manta_1_6_0	baseline	baseline	INV	> 0	0.05	0.83	0.99	0.9	0.2	417.67	20.0	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	INV	> 0	0.05	0.82	1.0	0.9	0.21	409.67	19.0	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	INV	> 0	0.04	0.85	1.0	0.92	0.08	435.67	21.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	> 0	0.06	0.8	1.0	0.89	0.21	401.33	19.0	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	INV	> 0	0.07	0.81	1.0	0.9	0.27	403.67	18.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	INV	> 0	0.07	0.81	1.0	0.9	0.25	403.0	18.67	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline	INV	1 - 100	0.0	0.0	0.0	0.0	0	0.0	0.0	0

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Precision avg.*	Prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	0.33	1
baseline	baseline	baseline	INV	101 - 500	0.0	1.0	0.0	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	101 - 500	0.0	1.0	0.33	2
baseline	baseline	baseline_or_manta_1_6_0	INV	101 - 500	0.02	0.99	0.33	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	INV	101 - 500	0.02	0.99	0.67	2
baseline	baseline_or_manta_1_6_0	baseline	INV	101 - 500	0.02	0.99	0.33	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	INV	101 - 500	0.02	0.99	0.67	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	INV	101 - 500	0.02	0.97	0.67	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	0.67	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	101 - 500	0.02	0.99	0.67	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	101 - 500	0.0	1.0	0.67	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	1.0	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	1.0	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	INV	101 - 500	0.02	0.99	1.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	INV	101 - 500	0.02	0.99	1.0	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	101 - 500	0.02	0.97	1.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	INV	101 - 500	0.02	0.97	1.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	101 - 500	0.0	1.0	0.67	5
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	0.67	2
baseline_and_delly_1_1_6	baseline	baseline	INV	101 - 500	0.0	1.0	0.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	0.67	2
baseline_and_manta_1_6_0	baseline	baseline	INV	101 - 500	0.0	1.0	0.33	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	INV	101 - 500	0.0	1.0	0.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	INV	101 - 500	0.0	1.0	0.67	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	101 - 500	0.0	1.0	0.67	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	INV	101 - 500	0.0	1.0	1.0	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	INV	101 - 500	0.0	1.0	1.0	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	INV	> 500	0.03	0.87	0.99	0.93	0.09	441.0	21.0	1
baseline	baseline	baseline	INV	> 500	0.05	0.83	0.99	0.9	0.18	420.67	20.0	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 500	0.03	0.87	0.99	0.93	0.09	441.0	21.0	2
baseline	baseline	baseline_or_manta_1_6_0	INV	> 500	0.05	0.87	0.97	0.91	0.1	438.67	21.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	INV	> 500	0.05	0.89	0.97	0.93	0.07	448.0	21.0	2
baseline	baseline_or_manta_1_6_0	baseline	INV	> 500	0.08	0.85	0.97	0.9	0.16	427.67	20.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	INV	> 500	0.05	0.89	0.97	0.93	0.07	448.33	21.0	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	INV	> 500	0.04	0.88	0.95	0.91	0.05	445.67	21.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	INV	> 500	0.03	0.89	0.99	0.94	0.06	447.67	21.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 500	0.06	0.9	0.97	0.93	0.06	450.33	21.0	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INV	> 500	0.03	0.89	0.99	0.94	0.06	447.67	21.0	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	INV	> 500	0.01	0.9	0.99	0.95	0.03	455.0	21.0	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	INV	> 500	0.01	0.9	0.99	0.94	0.03	452.33	21.0	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	INV	> 500	0.04	0.91	0.97	0.94	0.03	455.67	21.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	INV	> 500	0.04	0.9	0.97	0.93	0.03	454.67	21.0	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	INV	> 500	0.03	0.91	0.95	0.93	0.02	457.33	21.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	INV	> 500	0.04	0.9	0.95	0.92	0.05	452.33	21.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	> 500	0.06	0.81	1.0	0.89	0.26	387.0	18.33	5
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	INV	> 500	0.04	0.85	1.0	0.92	0.13	432.67	20.0	2
baseline_and_delly_1_1_6	baseline	baseline	INV	> 500	0.04	0.81	1.0	0.89	0.19	412.33	19.0	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	INV	> 500	0.03	0.87	0.99	0.92	0.11	438.0	21.0	2
baseline_and_manta_1_6_0	baseline	baseline	INV	> 500	0.05	0.83	0.99	0.9	0.2	417.67	20.0	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	INV	> 500	0.05	0.82	1.0	0.9	0.21	409.67	19.0	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	INV	> 500	0.04	0.85	1.0	0.92	0.08	435.67	21.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	INV	> 500	0.06	0.8	1.0	0.89	0.21	401.33	19.0	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	INV	> 500	0.07	0.81	1.0	0.9	0.27	403.67	18.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	INV	> 500	0.07	0.81	1.0	0.9	0.25	403.0	18.67	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	TRA	TRA	0.07	0.79	0.95	0.86	0.14	247.0	21.67	1
baseline	baseline	baseline	TRA	TRA	0.1	0.75	0.95	0.84	0.22	235.67	20.33	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	TRA	TRA	0.07	0.79	0.95	0.86	0.14	247.0	21.67	2
baseline	baseline	baseline_or_manta_1_6_0	TRA	TRA	0.11	0.8	0.88	0.84	0.18	252.33	21.67	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	TRA	TRA	0.12	0.82	0.88	0.85	0.15	257.67	22.0	2
baseline	baseline_or_manta_1_6_0	baseline	TRA	TRA	0.14	0.78	0.88	0.82	0.24	246.33	20.67	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	TRA	TRA	0.12	0.82	0.88	0.85	0.15	258.0	22.0	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	TRA	TRA	0.08	0.83	0.82	0.82	0.11	263.0	22.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	TRA	TRA	0.08	0.81	0.95	0.87	0.09	251.33	21.67	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	TRA	TRA	0.11	0.83	0.88	0.85	0.13	259.67	21.67	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	TRA	TRA	0.08	0.81	0.95	0.87	0.09	251.33	21.67	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	TRA	TRA	0.07	0.83	0.95	0.88	0.08	255.67	22.0	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	TRA	TRA	0.07	0.82	0.95	0.88	0.07	254.67	22.0	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	TRA	TRA	0.1	0.84	0.88	0.86	0.1	262.0	22.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	TRA	TRA	0.1	0.84	0.88	0.86	0.1	262.0	22.0	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	TRA	TRA	0.06	0.87	0.82	0.84	0.06	270.33	22.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	TRA	TRA	0.06	0.85	0.82	0.83	0.09	267.33	22.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	TRA	TRA	0.07	0.72	1.0	0.83	0.22	218.33	20.0	5
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	TRA	TRA	0.04	0.77	0.99	0.87	0.14	238.0	21.67	2
baseline_and_delly_1_1_6	baseline	baseline	TRA	TRA	0.05	0.73	0.99	0.84	0.18	226.67	20.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	TRA	TRA	0.05	0.78	0.96	0.86	0.13	246.0	21.67	2
baseline_and_manta_1_6_0	baseline	baseline	TRA	TRA	0.08	0.74	0.96	0.83	0.21	234.67	20.33	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	TRA	TRA	0.05	0.74	0.99	0.84	0.18	226.33	20.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	TRA	TRA	0.05	0.77	0.99	0.87	0.09	240.67	21.67	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	TRA	TRA	0.07	0.71	1.0	0.83	0.22	223.0	20.33	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	TRA	TRA	0.08	0.73	1.0	0.84	0.25	226.0	20.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	TRA	TRA	0.08	0.73	1.0	0.84	0.24	225.67	20.67	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	DEL	> 100	0.05	0.89	0.92	0.91	0.11	1062.33	66.67	2
baseline	baseline	baseline_or_gridss_2_13_2	DEL	> 100	0.07	0.91	0.93	0.92	0.09	1079.0	67.67	1
baseline	baseline	baseline	DEL	> 100	0.07	0.89	0.93	0.91	0.11	1060.0	66.67	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 100	0.11	0.91	0.88	0.89	0.09	1080.67	67.67	2
baseline	baseline	baseline_or_manta_1_6_0	DEL	> 100	0.09	0.91	0.91	0.91	0.08	1078.33	68.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DEL	> 100	0.03	0.93	0.89	0.91	0.04	1100.0	68.33	2
baseline	baseline_or_manta_1_6_0	baseline	DEL	> 100	0.05	0.91	0.89	0.9	0.08	1081.0	67.33	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 100	0.02	0.93	0.88	0.91	0.04	1102.0	68.67	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DEL	> 100	0.03	0.93	0.87	0.9	0.03	1099.33	68.67	2
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	DEL	> 100	0.04	0.94	0.91	0.92	0.04	1113.67	68.33	6
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DEL	> 100	0.07	0.92	0.93	0.92	0.07	1088.0	68.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 100	0.1	0.93	0.9	0.91	0.07	1093.33	68.33	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 100	0.12	0.92	0.88	0.9	0.07	1089.67	68.0	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	DEL	> 100	0.06	0.93	0.92	0.92	0.03	1104.0	68.67	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	DEL	> 100	0.03	0.94	0.88	0.91	0.02	1111.0	68.67	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DEL	> 100	0.02	0.94	0.89	0.91	0.03	1109.0	68.67	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 100	0.03	0.95	0.86	0.9	0.01	1114.33	69.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DEL	> 100	0.02	0.94	0.87	0.9	0.02	1108.33	69.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	> 100	0.03	0.87	1.0	0.93	0.19	981.0	65.0	5
baseline_and_delly_1_1_6	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 100	0.02	0.88	0.97	0.92	0.14	1026.67	64.33	6
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	DEL	> 100	0.06	0.9	0.96	0.93	0.11	1064.0	66.33	2
baseline_and_delly_1_1_6	baseline	baseline	DEL	> 100	0.04	0.88	0.96	0.92	0.11	1045.0	65.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	DEL	> 100	0.06	0.91	0.94	0.92	0.09	1077.33	67.67	2
baseline_and_manta_1_6_0	baseline	baseline	DEL	> 100	0.06	0.89	0.94	0.91	0.12	1058.33	66.67	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	DEL	> 100	0.05	0.89	0.96	0.92	0.12	1043.67	65.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DEL	> 100	0.06	0.89	0.97	0.93	0.11	1057.0	67.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	> 100	0.03	0.86	1.0	0.93	0.15	1007.33	65.33	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 100	0.04	0.88	0.98	0.93	0.16	1033.33	65.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DEL	> 100	0.04	0.88	0.99	0.93	0.15	1029.67	65.33	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	DEL	101 - 500	0.15	0.83	0.62	0.7	0.21	115.33	10.0	2
baseline	baseline	baseline_or_gridss_2_13_2	DEL	101 - 500	0.29	0.85	0.7	0.74	0.2	116.33	10.0	1
baseline	baseline	baseline	DEL	101 - 500	0.29	0.82	0.7	0.73	0.27	112.67	9.67	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	101 - 500	0.36	0.86	0.62	0.68	0.19	118.0	10.0	2
baseline	baseline	baseline_or_manta_1_6_0	DEL	101 - 500	0.33	0.86	0.65	0.71	0.19	118.67	10.33	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DEL	101 - 500	0.05	0.88	0.54	0.67	0.13	122.0	10.33	2
baseline	baseline_or_manta_1_6_0	baseline	DEL	101 - 500	0.09	0.86	0.55	0.66	0.2	118.33	10.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DEL	101 - 500	0.03	0.89	0.52	0.66	0.11	123.0	10.67	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DEL	101 - 500	0.06	0.9	0.5	0.64	0.06	124.33	10.67	2
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	DEL	101 - 500	0.08	0.89	0.58	0.7	0.09	122.67	10.67	6
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DEL	101 - 500	0.3	0.86	0.69	0.74	0.17	118.0	10.33	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	101 - 500	0.34	0.87	0.64	0.71	0.16	121.33	10.67	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	101 - 500	0.37	0.86	0.61	0.67	0.16	119.67	10.33	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	DEL	101 - 500	0.23	0.86	0.66	0.73	0.15	119.0	10.67	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	DEL	101 - 500	0.05	0.89	0.53	0.67	0.09	124.0	10.67	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DEL	101 - 500	0.05	0.89	0.54	0.67	0.1	123.67	10.67	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	101 - 500	0.06	0.91	0.49	0.64	0.03	127.0	11.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DEL	101 - 500	0.05	0.91	0.49	0.64	0.05	126.0	11.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	101 - 500	0.07	0.74	0.98	0.85	0.58	77.33	7.33	5
baseline_and_delly_1_1_6	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	101 - 500	0.05	0.81	0.79	0.8	0.22	109.0	9.33	6
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	DEL	101 - 500	0.21	0.83	0.79	0.8	0.22	112.67	9.67	2
baseline_and_delly_1_1_6	baseline	baseline	DEL	101 - 500	0.21	0.8	0.79	0.79	0.26	109.0	9.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	DEL	101 - 500	0.27	0.84	0.72	0.76	0.21	116.0	10.0	2
baseline_and_manta_1_6_0	baseline	baseline	DEL	101 - 500	0.27	0.81	0.72	0.75	0.27	112.33	9.67	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	DEL	101 - 500	0.22	0.81	0.79	0.79	0.26	109.0	9.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DEL	101 - 500	0.25	0.82	0.84	0.81	0.39	101.67	9.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	101 - 500	0.08	0.76	0.96	0.85	0.42	85.33	7.67	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	101 - 500	0.08	0.79	0.89	0.83	0.46	96.33	8.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DEL	101 - 500	0.06	0.79	0.9	0.84	0.45	95.33	8.33	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	DEL	> 500	0.02	0.91	0.99	0.95	0.1	956.33	60.33	2
baseline	baseline	baseline_or_gridss_2_13_2	DEL	> 500	0.02	0.93	0.99	0.96	0.08	972.0	61.0	1
baseline	baseline	baseline	DEL	> 500	0.02	0.91	0.99	0.95	0.1	956.0	60.33	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 500	0.05	0.93	0.97	0.95	0.08	972.0	61.0	2
baseline	baseline	baseline_or_manta_1_6_0	DEL	> 500	0.03	0.93	0.98	0.95	0.07	969.0	61.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DEL	> 500	0.02	0.94	0.98	0.96	0.04	987.67	61.67	2
baseline	baseline_or_manta_1_6_0	baseline	DEL	> 500	0.03	0.92	0.98	0.95	0.07	971.67	61.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 500	0.02	0.94	0.98	0.96	0.03	988.67	61.67	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DEL	> 500	0.02	0.94	0.97	0.95	0.03	984.67	61.67	2
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	DEL	> 500	0.02	0.95	0.99	0.97	0.03	1001.33	61.67	6
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DEL	> 500	0.02	0.94	0.99	0.96	0.06	980.0	61.33	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 500	0.04	0.94	0.98	0.96	0.06	982.0	61.33	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	> 500	0.05	0.94	0.96	0.95	0.06	980.0	61.33	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	DEL	> 500	0.01	0.95	0.98	0.97	0.02	995.33	62.0	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	DEL	> 500	0.02	0.95	0.97	0.96	0.01	997.33	62.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DEL	> 500	0.01	0.95	0.97	0.96	0.02	995.67	62.0	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DEL	> 500	0.01	0.96	0.96	0.96	0.01	997.67	62.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DEL	> 500	0.01	0.95	0.97	0.96	0.02	992.67	62.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	> 500	0.02	0.89	1.0	0.94	0.15	909.0	59.67	5
baseline_and_delly_1_1_6	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 500	0.02	0.9	1.0	0.95	0.13	925.67	58.33	6
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	DEL	> 500	0.03	0.92	1.0	0.95	0.1	960.33	60.0	2
baseline_and_delly_1_1_6	baseline	baseline	DEL	> 500	0.02	0.9	1.0	0.95	0.1	944.33	59.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	DEL	> 500	0.02	0.93	0.99	0.96	0.08	970.67	61.0	2
baseline_and_manta_1_6_0	baseline	baseline	DEL	> 500	0.02	0.91	0.99	0.95	0.1	954.67	60.33	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	DEL	> 500	0.01	0.91	1.0	0.95	0.1	943.0	59.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DEL	> 500	0.03	0.91	1.0	0.95	0.08	963.67	61.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DEL	> 500	0.02	0.89	1.0	0.94	0.12	928.0	60.0	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DEL	> 500	0.04	0.9	1.0	0.95	0.13	944.0	60.0	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DEL	> 500	0.04	0.9	1.0	0.95	0.12	941.33	60.0	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.89	0.99	0.94	0.12	1212.67	49.67	1
baseline	baseline	baseline	DUP	> 100	0.09	0.84	0.99	0.91	0.24	1129.0	47.67	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 100	0.03	0.89	0.99	0.94	0.12	1212.67	49.67	2
baseline	baseline	baseline_or_manta_1_6_0	DUP	> 100	0.02	0.89	0.99	0.93	0.13	1206.0	50.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DUP	> 100	0.05	0.91	0.99	0.95	0.07	1243.0	51.0	2
baseline	baseline_or_manta_1_6_0	baseline	DUP	> 100	0.11	0.85	0.99	0.91	0.23	1159.33	49.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 100	0.05	0.92	0.99	0.95	0.07	1246.0	51.33	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DUP	> 100	0.05	0.9	0.98	0.94	0.07	1236.33	51.33	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.92	0.99	0.95	0.08	1227.33	50.33	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 100	0.03	0.93	0.99	0.96	0.09	1238.0	50.67	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 100	0.03	0.92	0.99	0.95	0.08	1227.33	50.33	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.93	0.99	0.96	0.07	1242.33	51.33	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.93	0.99	0.96	0.02	1256.0	51.67	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.94	0.99	0.96	0.03	1262.0	51.67	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.93	0.99	0.96	0.04	1257.67	51.67	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 100	0.01	0.95	0.98	0.97	0.03	1268.33	52.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DUP	> 100	0.04	0.93	0.98	0.95	0.06	1251.0	52.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	> 100	0.13	0.8	1.0	0.88	0.25	1053.33	45.0	5
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	DUP	> 100	0.05	0.88	1.0	0.93	0.13	1183.67	48.67	2
baseline_and_delly_1_1_6	baseline	baseline	DUP	> 100	0.08	0.82	1.0	0.9	0.21	1100.0	46.67	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	DUP	> 100	0.03	0.89	1.0	0.94	0.13	1204.67	49.67	2
baseline_and_manta_1_6_0	baseline	baseline	DUP	> 100	0.09	0.83	1.0	0.91	0.24	1121.0	47.67	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	DUP	> 100	0.09	0.83	1.0	0.9	0.21	1095.67	46.67	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DUP	> 100	0.07	0.87	1.0	0.93	0.12	1193.33	48.67	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	> 100	0.12	0.79	1.0	0.88	0.25	1086.33	45.67	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 100	0.12	0.82	1.0	0.9	0.27	1127.0	47.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DUP	> 100	0.12	0.82	1.0	0.9	0.27	1115.0	47.0	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	DUP	101 - 500	0.16	0.79	1.0	0.87	0.55	43.67	2.0	1
baseline	baseline	baseline	DUP	101 - 500	0.37	0.6	1.0	0.7	0.87	32.33	1.67	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	101 - 500	0.16	0.79	1.0	0.87	0.55	43.67	2.0	2
baseline	baseline	baseline_or_manta_1_6_0	DUP	101 - 500	0.19	0.75	1.0	0.85	0.44	41.33	2.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DUP	101 - 500	0.18	0.79	1.0	0.88	0.53	44.67	2.0	2
baseline	baseline_or_manta_1_6_0	baseline	DUP	101 - 500	0.37	0.61	1.0	0.71	0.87	33.33	1.67	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DUP	101 - 500	0.19	0.83	1.0	0.9	0.38	47.33	2.0	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DUP	101 - 500	0.21	0.76	1.0	0.86	0.4	42.33	2.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DUP	101 - 500	0.1	0.88	1.0	0.93	0.24	49.67	2.0	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	101 - 500	0.02	0.93	1.0	0.96	0.09	52.67	2.0	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	101 - 500	0.1	0.88	1.0	0.93	0.24	49.67	2.0	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	DUP	101 - 500	0.11	0.88	1.0	0.94	0.2	50.33	2.0	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	DUP	101 - 500	0.11	0.88	1.0	0.94	0.2	50.33	2.0	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	DUP	101 - 500	0.11	0.89	1.0	0.94	0.2	50.67	2.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DUP	101 - 500	0.11	0.89	1.0	0.94	0.2	50.67	2.0	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	101 - 500	0.04	0.94	1.0	0.97	0.04	53.67	2.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DUP	101 - 500	0.18	0.85	1.0	0.92	0.33	48.33	2.0	3
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	DUP	101 - 500	0.36	0.67	1.0	0.77	0.87	34.67	1.67	2
baseline_and_delly_1_1_6	baseline	baseline	DUP	101 - 500	0.44	0.49	1.0	0.59	0.87	23.33	1.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	DUP	101 - 500	0.17	0.78	1.0	0.87	0.58	43.33	2.0	2
baseline_and_manta_1_6_0	baseline	baseline	DUP	101 - 500	0.36	0.59	1.0	0.69	0.87	32.0	1.67	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	DUP	101 - 500	0.43	0.5	1.0	0.6	0.87	23.33	1.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DUP	101 - 500	0.28	0.71	1.0	0.81	0.56	40.67	2.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	101 - 500	0.43	0.5	1.0	0.6	0.89	29.33	1.67	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DUP	101 - 500	0.43	0.51	1.0	0.62	0.87	29.33	1.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DUP	101 - 500	0.42	0.52	1.0	0.63	0.87	30.0	1.67	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline_or_gridss_2_13_2	DUP	> 500	0.02	0.92	0.99	0.95	0.1	1172.0	47.67	1
baseline	baseline	baseline	DUP	> 500	0.04	0.89	0.99	0.94	0.22	1098.33	46.0	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 500	0.02	0.92	0.99	0.95	0.1	1172.0	47.67	2
baseline	baseline	baseline_or_manta_1_6_0	DUP	> 500	0.02	0.91	0.98	0.95	0.12	1167.33	48.0	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DUP	> 500	0.02	0.93	0.98	0.96	0.06	1201.67	49.0	2
baseline	baseline_or_manta_1_6_0	baseline	DUP	> 500	0.05	0.91	0.98	0.94	0.2	1128.0	47.33	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 500	0.03	0.94	0.98	0.96	0.06	1202.0	49.33	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DUP	> 500	0.02	0.93	0.98	0.95	0.06	1197.0	49.33	2
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DUP	> 500	0.03	0.93	0.99	0.96	0.08	1181.33	48.33	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 500	0.04	0.93	0.98	0.96	0.09	1189.0	48.67	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DUP	> 500	0.03	0.93	0.99	0.96	0.08	1181.33	48.33	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	DUP	> 500	0.01	0.94	0.99	0.97	0.06	1196.0	49.33	6
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	DUP	> 500	0.01	0.94	0.99	0.97	0.01	1209.67	49.67	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	DUP	> 500	0.02	0.95	0.98	0.97	0.02	1215.33	49.67	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	DUP	> 500	0.02	0.94	0.98	0.96	0.03	1211.0	49.67	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	DUP	> 500	0.01	0.95	0.98	0.97	0.03	1218.67	50.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	DUP	> 500	0.02	0.94	0.98	0.96	0.05	1206.33	50.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	> 500	0.04	0.87	0.99	0.93	0.22	1034.0	44.0	5
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	DUP	> 500	0.03	0.91	0.99	0.95	0.1	1151.67	47.0	2
baseline_and_delly_1_1_6	baseline	baseline	DUP	> 500	0.03	0.88	0.99	0.93	0.18	1078.0	45.33	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	DUP	> 500	0.02	0.91	0.99	0.95	0.11	1164.67	47.67	2
baseline_and_manta_1_6_0	baseline	baseline	DUP	> 500	0.03	0.89	0.99	0.94	0.21	1091.0	46.0	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	DUP	> 500	0.04	0.89	0.99	0.94	0.18	1073.67	45.33	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	DUP	> 500	0.03	0.91	0.99	0.95	0.11	1156.0	46.67	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	DUP	> 500	0.04	0.87	0.99	0.93	0.23	1059.33	44.0	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	DUP	> 500	0.05	0.89	0.99	0.94	0.24	1100.33	46.0	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	DUP	> 500	0.05	0.89	0.99	0.94	0.24	1087.67	45.33	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	SV	ALL	0.06	0.84	0.96	0.89	0.17	2615.33	134.67	2
baseline	baseline	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.87	0.96	0.91	0.1	2731.67	139.0	1
baseline	baseline	baseline	SV	ALL	0.07	0.84	0.96	0.89	0.18	2613.33	134.67	0
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	SV	ALL	0.06	0.87	0.94	0.9	0.1	2732.67	139.0	2
baseline	baseline	baseline_or_manta_1_6_0	SV	ALL	0.06	0.87	0.93	0.9	0.1	2726.0	139.33	1
baseline	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	SV	ALL	0.05	0.89	0.93	0.91	0.06	2791.0	141.0	2
baseline	baseline_or_manta_1_6_0	baseline	SV	ALL	0.08	0.86	0.93	0.89	0.15	2672.67	136.67	1
baseline	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_(manta_1_6_0_and_svaba_1_1_0))	SV	ALL	0.05	0.9	0.92	0.91	0.06	2793.67	141.33	4
baseline	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	SV	ALL	0.04	0.89	0.9	0.9	0.05	2785.33	141.33	2
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_or_manta_1_6_0)_and_(delly_1_1_6_or_svaba_1_1_0))	baseline_or_gridss_2_13_2	SV	ALL	0.03	0.91	0.95	0.93	0.05	2802.33	141.0	6
baseline_or_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.89	0.96	0.92	0.07	2758.67	139.67	2
baseline_or_gridss_2_13_2	baseline	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	SV	ALL	0.07	0.9	0.93	0.91	0.08	2778.33	140.0	3
baseline_or_gridss_2_13_2	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	SV	ALL	0.06	0.89	0.94	0.91	0.07	2759.67	139.67	3
baseline_or_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.9	0.96	0.93	0.03	2806.0	141.67	5
baseline_or_gridss_2_13_2	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.91	0.92	0.92	0.03	2824.67	141.67	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.91	0.93	0.92	0.03	2818.0	141.67	3
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_(gridss_2_13_2_or_manta_1_6_0)	SV	ALL	0.03	0.92	0.9	0.91	0.02	2837.67	142.0	4
baseline_or_gridss_2_13_2	baseline_or_manta_1_6_0	baseline_or_manta_1_6_0	SV	ALL	0.03	0.91	0.9	0.9	0.04	2812.33	142.0	3
baseline_and_((brass_6_3_4_or_cgppindel_3_9_0)_and_gridss_2_13_2)	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	SV	ALL	0.06	0.81	1.0	0.89	0.22	2434.67	130.0	5
baseline_and_delly_1_1_6	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	SV	ALL	0.05	0.82	0.99	0.89	0.19	2511.67	130.0	6
baseline_and_delly_1_1_6	baseline	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.86	0.98	0.91	0.11	2677.67	136.33	2
baseline_and_delly_1_1_6	baseline	baseline	SV	ALL	0.04	0.82	0.98	0.89	0.16	2559.33	132.0	1
baseline_and_manta_1_6_0	baseline	baseline_or_gridss_2_13_2	SV	ALL	0.04	0.87	0.97	0.91	0.1	2719.33	139.0	2
baseline_and_manta_1_6_0	baseline	baseline	SV	ALL	0.06	0.83	0.97	0.89	0.17	2601.0	134.67	1
baseline_and_(delly_1_1_6_and_manta_1_6_0)	baseline	baseline	SV	ALL	0.05	0.83	0.98	0.9	0.16	2551.67	132.0	2
baseline_and_gridss_2_13_2	baseline	baseline_or_gridss_2_13_2	SV	ALL	0.05	0.85	0.99	0.91	0.1	2688.33	138.0	2
baseline_and_gridss_2_13_2	baseline	baseline_and_(gridss_2_13_2_and_svaba_1_1_0)	SV	ALL	0.06	0.8	1.0	0.89	0.2	2503.67	131.67	3
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_(delly_1_1_6_and_(manta_1_6_0_and_svaba_1_1_0))	SV	ALL	0.07	0.82	0.99	0.9	0.22	2567.67	133.67	7
baseline_and_gridss_2_13_2	baseline_or_((brass_6_3_4_and_svaba_1_1_0)_or_gridss_2_13_2)	baseline_and_((cgppindel_3_9_0_or_gridss_2_13_2)_and_(delly_1_1_6_and_svaba_1_1_0))	SV	ALL	0.07	0.82	0.99	0.9	0.21	2553.33	133.0	8

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline	baseline	SNV	1	0.12	0.81	0.97	0.88	0.24	217.0	12.0	0
baseline	baseline	baseline_or_(muse_2_0_or_sage_3_0)	SNV	1	0.12	0.82	0.96	0.88	0.25	219.67	12.0	2
baseline	baseline	baseline_or_sage_3_0	SNV	1	0.12	0.82	0.97	0.89	0.24	218.67	12.0	1
baseline	baseline_or_muse_2_0	baseline	SNV	1	0.04	0.86	0.96	0.91	0.14	228.33	12.67	1
baseline	baseline_or_(cgpcavemanwrapper_1_16_0_and_gatk_4_2_6_1)	baseline	SNV	1	0.04	0.87	0.97	0.92	0.09	232.0	13.33	2
baseline	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	SNV	1	0.04	0.87	0.97	0.92	0.09	231.67	13.33	2
baseline_or_sage_3_0	baseline	baseline	SNV	1	0.12	0.82	0.97	0.89	0.23	219.33	12.0	1
baseline_or_sage_3_0	baseline	baseline_or_(muse_2_0_or_sage_3_0)	SNV	1	0.13	0.83	0.96	0.89	0.23	222.0	12.0	3
baseline_or_sage_3_0	baseline	baseline_or_sage_3_0	SNV	1	0.13	0.83	0.97	0.89	0.22	221.0	12.0	2
baseline_or_sage_3_0	baseline_or_(cgpcavemanwrapper_1_16_0_and_gatk_4_2_6_1)	baseline	SNV	1	0.04	0.88	0.97	0.92	0.08	234.33	13.33	3
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	SNV	1	0.04	0.88	0.97	0.92	0.09	234.0	13.33	3
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline_or_sage_3_0	SNV	1	0.04	0.89	0.97	0.92	0.07	235.67	13.33	4

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	INDEL	1 - 100	0.05	0.7	0.95	0.81	0.22	128.33	17.67	2
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_or_sage_3_0	INDEL	1 - 100	0.07	0.73	0.95	0.83	0.21	131.33	18.0	3
baseline	baseline	baseline	INDEL	1 - 100	0.04	0.69	0.95	0.8	0.27	123.67	17.0	0
baseline	baseline	baseline_or_(muse_2_0_or_sage_3_0)	INDEL	1 - 100	0.08	0.72	0.95	0.82	0.27	126.67	17.33	2
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INDEL	1 - 100	0.07	0.71	0.91	0.79	0.3	126.67	17.0	2
baseline	baseline	baseline_or_sage_3_0	INDEL	1 - 100	0.08	0.72	0.95	0.82	0.27	126.67	17.33	1
baseline	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	INDEL	1 - 100	0.08	0.72	0.95	0.82	0.18	129.33	17.67	2
baseline	baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	baseline_or_sage_3_0	INDEL	1 - 100	0.07	0.75	0.95	0.83	0.21	131.33	18.0	3
baseline_or_sage_3_0	baseline	baseline	INDEL	1 - 100	0.1	0.74	0.95	0.83	0.24	128.0	17.33	1
baseline_or_sage_3_0	baseline	baseline_or_(muse_2_0_or_sage_3_0)	INDEL	1 - 100	0.09	0.77	0.95	0.85	0.19	131.0	17.67	3
baseline_or_sage_3_0	baseline	baseline_or_sage_3_0	INDEL	1 - 100	0.09	0.77	0.95	0.85	0.19	131.0	17.67	2
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	INDEL	1 - 100	0.08	0.77	0.95	0.85	0.15	133.67	18.0	3
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline_or_sage_3_0	INDEL	1 - 100	0.04	0.8	0.95	0.87	0.08	136.67	18.33	4

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	DEL	1 - 100	0.04	0.74	0.95	0.83	0.19	92.0	15.33	2
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_or_sage_3_0	DEL	1 - 100	0.06	0.77	0.95	0.85	0.19	93.67	15.33	3
baseline	baseline	baseline	DEL	1 - 100	0.05	0.72	0.95	0.82	0.23	89.67	15.0	0
baseline	baseline	baseline_or_(muse_2_0_or_sage_3_0)	DEL	1 - 100	0.07	0.75	0.95	0.84	0.24	91.33	15.0	2
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	DEL	1 - 100	0.06	0.73	0.91	0.81	0.24	90.67	15.0	2
baseline	baseline	baseline_or_sage_3_0	DEL	1 - 100	0.07	0.75	0.95	0.84	0.24	91.33	15.0	1
baseline	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	DEL	1 - 100	0.06	0.76	0.95	0.84	0.16	93.0	15.33	2
baseline	baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	baseline_or_sage_3_0	DEL	1 - 100	0.05	0.77	0.95	0.85	0.18	93.67	15.33	3
baseline_or_sage_3_0	baseline	baseline	DEL	1 - 100	0.09	0.76	0.95	0.85	0.2	92.67	15.0	1
baseline_or_sage_3_0	baseline	baseline_or_(muse_2_0_or_sage_3_0)	DEL	1 - 100	0.09	0.79	0.95	0.86	0.16	94.33	15.0	3
baseline_or_sage_3_0	baseline	baseline_or_sage_3_0	DEL	1 - 100	0.09	0.79	0.95	0.86	0.16	94.33	15.0	2
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	DEL	1 - 100	0.07	0.8	0.95	0.87	0.12	96.0	15.33	3
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline_or_sage_3_0	DEL	1 - 100	0.05	0.82	0.95	0.88	0.07	97.67	15.33	4

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

center_a	center_b	center_c	Variant type	Variant size	PHS	Recall avg.*	Precision avg.*	F1 score avg.	GDR	Prot. genes avg.*	Cancer driver prot. genes avg.*	Total added callers
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline	INS/DUP	1 - 100	0.07	0.65	0.95	0.77	0.3	39.0	4.67	2
baseline	baseline_or_(cgppindel_3_9_0_and_svaba_1_1_0)	baseline_or_sage_3_0	INS/DUP	1 - 100	0.08	0.7	0.95	0.8	0.28	41.0	5.33	3
baseline	baseline	baseline	INS/DUP	1 - 100	0.06	0.64	0.95	0.77	0.38	36.33	4.33	0
baseline	baseline	baseline_or_(muse_2_0_or_sage_3_0)	INS/DUP	1 - 100	0.09	0.69	0.95	0.8	0.37	38.33	5.0	2
baseline	baseline	baseline_or_(cgppindel_3_9_0_or_gridss_2_13_2)	INS/DUP	1 - 100	0.09	0.68	0.91	0.77	0.44	38.67	4.33	2
baseline	baseline	baseline_or_sage_3_0	INS/DUP	1 - 100	0.09	0.69	0.95	0.8	0.37	38.33	5.0	1
baseline	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	INS/DUP	1 - 100	0.1	0.67	0.95	0.79	0.26	39.0	4.67	2
baseline	baseline_or_(cgppindel_3_9_0_and_strelka_2_9_10)	baseline_or_sage_3_0	INS/DUP	1 - 100	0.1	0.72	0.95	0.82	0.29	41.0	5.33	3
baseline_or_sage_3_0	baseline	baseline	INS/DUP	1 - 100	0.1	0.7	0.95	0.8	0.37	38.33	5.0	1
baseline_or_sage_3_0	baseline	baseline_or_(muse_2_0_or_sage_3_0)	INS/DUP	1 - 100	0.08	0.75	0.95	0.83	0.26	40.33	5.67	3
baseline_or_sage_3_0	baseline	baseline_or_sage_3_0	INS/DUP	1 - 100	0.08	0.75	0.95	0.83	0.26	40.33	5.67	2
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline	INS/DUP	1 - 100	0.11	0.73	0.95	0.82	0.24	41.0	5.33	3
baseline_or_sage_3_0	baseline_or_(gatk_4_2_6_1_and_strelka_2_9_10)	baseline_or_sage_3_0	INS/DUP	1 - 100	0.04	0.78	0.94	0.85	0.11	43.0	6.0	4

*Recall avg.: Recall is calculated exclusively using the true positives and false negatives from the recall samples.

*Precision avg.: Precision is calculated exclusively using the true positives and false positives from the precision samples.

*Prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

*Cancer driver prot. genes avg.: Warning: ONCOLINER does not compute genes linked to false positives.

Assessment

Assessment overview: center_a

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

Assessment by sample: center_a

mosaic_genome_PCAWG_2 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_PCAWG_1 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_PCAWG_0 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_HMF (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

tumorized_precision_NA12878 (precision)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

tumorized_precision_HG002 (precision)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

Assessment overview: center_b

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

Assessment by sample: center_b

mosaic_genome_PCAWG_2 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_PCAWG_1 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_PCAWG_0 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_HMF (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

tumorized_precision_NA12878 (precision)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

tumorized_precision_HG002 (precision)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

Assessment overview: center_c

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

Assessment by sample: center_c

mosaic_genome_PCAWG_2 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_PCAWG_1 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_PCAWG_0 (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

mosaic_genome_HMF (recall)

Performance metrics (By SNV, indel and SV)

Performance metrics (By variant type)

Performance metrics (By variant type and size)

SV

SV

SV

SV