GUIDANCE accepts PLINK format files, e.g. gwas.bed, gwas.bim, gwas.fam), as input. It also accepts covariates, such as principal compontents, gender or any covariate defined in the sample file. As part of the input, GUIDANCE also requires the inclusion of one, or several reference panels for imputation accepting public (1KG phase 1 or 3, HapMap, DCEG, UK10K, GoNL) or private reference panels. Also a genetic map is needed.

Sample File

The user needs to also provide an adequate sample file. Please, check SNPTESTv2 webpage for information on how to prepare a suitable sample file.

Genetic Map File

All of IMPUTE2 reference panel download packages come with appropriate recombination map files. Check IMPUTE2 webpage for more information. Hence, this genetic map files can be used for phasing with SHAPEIT. A file per chromosome must be given.

On the other hand, when phasing with EAGLE, a single file must be given. Several compatible options are available on the Broad Website.

Reference panels

It must be noted that, when using IMPUTE2, the reference panels must be given with format .haps and .leg. On the other hand, Minimac4 only accepts M3VCF. Regular VCF can be converted to M3VCF using Minimac3.

In addition, we have encountered some problems when imputing the ChrX with Minimac4. This is why the imputation of this chromosome is always done with IMPUTE2, so even when using Minimac4 both .haps and .legend must be given for ChrX if this chromosome is included in the study.

We give some templates of configuration files for a study from Chr21 to ChrX, using HRC, 1kphase3, uk10k and gonl as reference panels and Eagle-IMPUTE2, SHAPEIT-IMPUTE2, Eagle-Minimac4 and SHAPEIT-Minimac4 as phasing and imputation tools.

#!/bin/bash

### PHASE 1 ###

export phasingMem="50.0"
export phasingCU="48"
export phasingBedMem="50.0"
export phasingBedCU="48"

### PHASE 2 ###

export qctoolMem="16.0"
export qctoolSMem="1.0"
export gtoolsMem="6.0"
export samtoolsBgzipMem="6.0"
export imputeWithImputeLowMem="8.0"
export imputeWithImputeMediumMem="12.0"
export imputeWithImputeHighMem="20.0"
export imputeWithMinimacLowMem="4.0"
export imputeWithMinimacMediumMem="8.0"
export imputeWithMinimacHighMem="32.0"
export filterByInfoImputeMem="12.0"
export filterByInfoMinimacMem="24.0"

### PHASE 3 ###

export createListOfExcludedSnpsMem="1.0"
export filterHaplotypesMem="1.0"
export filterByAllMem="1.0"
export jointFilteredByAllFilesMem="15.0"
export jointCondensedFilesMem="1.0"
export generateTopHitsAllMem="2.0"
export generateTopHitsMem="2.0"
export filterByMafMem="2.0"
export snptestMem="2.0"
export mergeTwoChunksMem="1.0"
export mergeTwoChunksInTheFirstMem="1.0"
export combinePanelsMem="1.0"
export combineCondensedFilesMem="1.0"
export combinePanelsComplex1Mem="1.0"


### PHASE 4 ###

export generateCondensedTopHitsCU="48"
export generateCondensedTopHitsMem="90.0"
export generateQQManhattanPlotsCU="24"
export generateQQManhattanPlotsMem="45.0"
export phenoMergeMem="80.0"

#!/bin/bash -e

export COMPSS_PYTHON_VERSION="2"

module purge
module load intel/2018.1
module load singularity/2.4.2

base_dir=$(pwd)
work_dir=${base_dir}/logs/
worker_work_dir=${base_dir}/tmpForCOMPSs/
worker_work_dir=scratch

source $base_dir/set_environment.sh

exec_time=2880
num_nodes=50
tracing=true
graph=true
debug=off
cpus_per_node=48
worker_in_master_cpus=0
worker_in_master_memory=80000
qos=bsc_cs

mkdir -p ${base_dir}/outputs_directory

/path/to/COMPSs/Runtime/scripts/user/enqueue_compss \
--qos=${qos} \
--job_dependency=5804941 \
--graph=${graph} \
--tracing=${tracing} \
--log_level=${debug} \
--exec_time=${exec_time} \
--num_nodes=${num_nodes} \
--base_log_dir=${base_dir} \
--worker_in_master_cpus=${worker_in_master_cpus} \
--worker_in_master_memory=${worker_in_master_memory} \
--cpus_per_node=${cpus_per_node} \
--master_working_dir=${work_dir} \
--worker_working_dir=${worker_work_dir} \
--scheduler="es.bsc.compss.scheduler.fifodatanew.FIFODataScheduler" \
--classpath=/path/to/guidance.jar \
--jvm_workers_opts="-Dcompss.worker.removeWD=true" \
--container_image=/path/to/guidance_singularity.img \
guidance.Guidance -config_file ${base_dir}/config_GERA_5000_shapeit_impute_1_23_cloud.file

#!/bin/bash -e

module load COMPSs
module load mkl
module load intel/2017.4
module load samtools/1.5
module load R/3.5.1
module load bcftools/1.8
module load gcc/5.4.0

base_dir=$(pwd)
work_dir=${base_dir}/logs/
worker_work_dir=${base_dir}/tmpForCOMPSs/

export BCFTOOLSBINARY=/path/to/BCFTOOLS/1.8/INTEL/bin/bcftools
export RSCRIPTBINDIR=/path/to/R/3.5.1/INTEL/bin/
export SAMTOOLSBINARY=/path/to/SAMTOOLS/1.5-DNANEXUS/INTEL/IMPI/bin

export PLINKBINARY=/path/to/TOOLS/apps_gwimp_compss/plink_1.9/plink
export EAGLEBINARY=/path/to/TOOLS/Eagle_v2.4.1/eagle
export RSCRIPTDIR=/path/to/R_SCRIPTS/
export QCTOOLBINARY=/path/to/TOOLS/qctool_v1.4-linux-x86_64/qctool
export SHAPEITBINARY=/path/to/TOOLS/shapeit.v2.r727.linux.x64
export IMPUTE2BINARY=/path/to/TOOLS/impute_v2.3.2_x86_64_static/impute2
export SNPTESTBINARY=/path/to/TOOLS/snptest_v2.5
export MINIMAC3BINARY=/path/to/TOOLS/Minimac3/bin/Minimac3
export MINIMAC4BINARY=/path/toTOOLS//Minimac4/release-build/minimac4
export TABIXBINARY=/path/to/SAMTOOLS/1.5-DNANEXUS/INTEL/IMPI/bin/tabix
export BGZIPBINARY=/path/to/SAMTOOLS/1.5-DNANEXUS/INTEL/IMPI/bin/bgzip

export R_LIBS_USER=/path/to/TOOLS/R_libs/

export LC_ALL="C"

source $base_dir/set_environment.sh

exec_time=700
num_nodes=25
tracing=true
graph=true
log_level=off
cpus_per_node=48
worker_in_master_cpus=0
worker_in_master_memory=80000
qos=bsc_cs

mkdir -p ${base_dir}/outputs_shapeit_impute_1909_erase_all

enqueue_compss \
--qos=${qos} \
--job_dependency=7403259 \
--graph=${graph} \
--tracing=${tracing} \
--log_level=${log_level} \
--exec_time=${exec_time} \
--num_nodes=${num_nodes} \
--base_log_dir=${base_dir} \
--worker_in_master_cpus=${worker_in_master_cpus} \
--worker_in_master_memory=${worker_in_master_memory} \
--cpus_per_node=${cpus_per_node} \
--master_working_dir=${work_dir} \
--worker_working_dir=${worker_work_dir} \
--scheduler="es.bsc.compss.scheduler.fifodatanew.FIFODataScheduler" \
--classpath=${base_dir}/guidance_25_1909_erase.jar \
--jvm_workers_opts="-Dcompss.worker.removeWD=true" \
guidance.Guidance -config_file ${base_dir}/config_GERA_300_shapeit_impute_1909_erase_all.file