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oicr-gsi / gatk-genotype-GVCFs

Genotype GVCFs WDL workflow for GATK4

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genotypeGVCFs

Workflow to run GATK GenotypeGVCFs

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run genotypeGVCFs.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
vcfIndices Array[File] The indices for the vcf files to be used.
vcfs Array[File] The vcf files to be used.
intervalsToParallelizeBy String Comma separated list of intervals to split by (e.g. chr1,chr2,chr3,chr4).
callGenotypeGVCFs.dbsnpFilePath String The dbSNP VCF to call against.
callGenotypeGVCFs.refFasta String The file path to the reference genome.
indelsVariantRecalibrator.modules String Required environment modules.
indelsVariantRecalibrator.mills_vcf String Mills and 1000G indels vcf file.
indelsVariantRecalibrator.mills_vcf_index String Mills and 1000G indels vcf index file.
indelsVariantRecalibrator.axiomPoly_vcf String AxiomPoly vcf file.
indelsVariantRecalibrator.axiomPoly_index String AxiomPoly vcf index file
indelsVariantRecalibrator.dbsnp_vcf String dbsnp vcf.
indelsVariantRecalibrator.dbsnp_vcf_index String dbsnp vcf index file.
snpsVariantRecalibrator.modules String Required environment modules.
snpsVariantRecalibrator.hapmap_vcf String hapmap vcf file.
snpsVariantRecalibrator.omni_vcf String 1000G omni vcf file.
snpsVariantRecalibrator.one_thousand_genomes_vcf String 1000G snps vcf file.
snpsVariantRecalibrator.dbsnp_vcf String dbsnp vcf file.
snpsVariantRecalibrator.hapmap_vcf_index String hapmap vcf index file.
snpsVariantRecalibrator.omni_vcf_index String 1000G omni vcf index file.
snpsVariantRecalibrator.one_thousand_genomes_vcf_index String 1000G snps vcf index file.
snpsVariantRecalibrator.dbsnp_vcf_index String dbsnp vcf index file.
collectVariantCallingMetrics.dbsnp_vcf String The dbsnp vcf file.
collectVariantCallingMetrics.dbsnp_vcf_index String The dbsnp vcf index file.
collectVariantCallingMetrics.ref_dict String The sequence dictionary file for speed loading of the dbsnp file.
collectVariantCallingMetrics.modules String Required environment modules.

Optional workflow parameters:

Parameter Value Default Description
outputFileNamePrefix String "output" Prefix for output file.
doHardFilter Boolean false If true, do hard filtering.
doVQSR Boolean false If true, run VQSR.

Optional task parameters:

Parameter Value Default Description
splitStringToArray.lineSeparator String "," line separator for intervalsToParallelizeBy.
splitStringToArray.jobMemory Int 1 Memory allocated to job (in GB).
splitStringToArray.cores Int 1 The number of cores to allocate to the job.
splitStringToArray.timeout Int 1 Maximum amount of time (in hours) the task can run for.
callGenomicsDBImport.extraArgs String? None Additional arguments to be passed directly to the command.
callGenomicsDBImport.modules String "gatk/4.1.7.0" Required environment modules.
callGenomicsDBImport.jobMemory Int 24 Memory allocated to job (in GB).
callGenomicsDBImport.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
callGenomicsDBImport.cores Int 1 The number of cores to allocate to the job.
callGenomicsDBImport.timeout Int 48 Maximum amount of time (in hours) the task can run for.
callGenotypeGVCFs.extraArgs String? None Additional arguments to be passed directly to the command.
callGenotypeGVCFs.standCallConf Float 30.0 The minimum phred-scaled confidence threshold at which variants should be called.
callGenotypeGVCFs.modules String "gatk/4.1.7.0" Required environment modules.
callGenotypeGVCFs.jobMemory Int 24 Memory allocated to job (in GB).
callGenotypeGVCFs.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
callGenotypeGVCFs.cores Int 1 The number of cores to allocate to the job.
callGenotypeGVCFs.timeout Int 48 Maximum amount of time (in hours) the task can run for.
gatherVcfs.modules String "gatk/4.1.7.0 tabix/0.2.6" Required environment modules.
gatherVcfs.extraArgs String? None Additional arguments to be passed directly to the command.
gatherVcfs.jobMemory Int 24 Memory allocated to job (in GB).
gatherVcfs.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
gatherVcfs.cores Int 1 The number of cores to allocate to the job.
gatherVcfs.timeout Int 24 Maximum amount of time (in hours) the task can run for.
hardFilter.excess_het_threshold Float 54.69 Filtering threshold on ExcessHet.
hardFilter.extraArgs String? None Additional arguments to be passed directly to the command.
hardFilter.modules String "gatk/4.1.7.0" Required environment modules.
hardFilter.jobMemory Int 12 Memory allocated to job (in GB).
hardFilter.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
hardFilter.cores Int 1 The number of cores to allocate to the job.
hardFilter.timeout Int 48 Maximum amount of time (in hours) the task can run for.
makeSitesOnlyVcf.modules String "gatk/4.1.7.0" Required environment modules.
makeSitesOnlyVcf.extraArgs String? None Additional arguments to be passed directly to the command.
makeSitesOnlyVcf.jobMemory Int 12 Memory allocated to job (in GB).
makeSitesOnlyVcf.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
makeSitesOnlyVcf.cores Int 1 The number of cores to allocate to the job.
makeSitesOnlyVcf.timeout Int 48 Maximum amount of time (in hours) the task can run for.
indelsVariantRecalibrator.recalibration_tranche_values Array[String] ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"] The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent).
indelsVariantRecalibrator.recalibration_annotation_values Array[String] ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"] The names of the annotations which should used for calculations.
indelsVariantRecalibrator.max_gaussians Int 4 the expected number of clusters in modeling.
indelsVariantRecalibrator.extraArgs String? None Additional arguments to be passed directly to the command.
indelsVariantRecalibrator.jobMemory Int 24 Memory allocated to job (in GB).
indelsVariantRecalibrator.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
indelsVariantRecalibrator.cores Int 1 The number of cores to allocate to the job.
indelsVariantRecalibrator.timeout Int 24 Maximum amount of time (in hours) the task can run for.
snpsVariantRecalibrator.recalibration_tranche_values Array[String] ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"] The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent).
snpsVariantRecalibrator.recalibration_annotation_values Array[String] ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"] The names of the annotations which should used for calculations.
snpsVariantRecalibrator.extraArgs String? None Additional arguments to be passed directly to the command.
snpsVariantRecalibrator.max_gaussians Int 6 the expected number of clusters in modeling.
snpsVariantRecalibrator.jobMemory Int 24 Memory allocated to job (in GB).
snpsVariantRecalibrator.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
snpsVariantRecalibrator.cores Int 1 The number of cores to allocate to the job.
snpsVariantRecalibrator.timeout Int 48 Maximum amount of time (in hours) the task can run for.
applyRecalibration.modules String "gatk/4.1.7.0" Required environment modules.
applyRecalibration.indel_filter_level Float 99.7 The truth sensitivity level at which to start filtering indels.
applyRecalibration.snp_filter_level Float 99.7 The truth sensitivity level at which to start filtering snps.
applyRecalibration.extraArgsIndel String? None Additional arguments for the indel mode.
applyRecalibration.extraArgsSNP String? None Additional arguments for the snp mode.
applyRecalibration.jobMemory Int 24 Memory allocated to job (in GB).
applyRecalibration.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
applyRecalibration.cores Int 1 The number of cores to allocate to the job.
applyRecalibration.timeout Int 48 Maximum amount of time (in hours) the task can run for.
collectVariantCallingMetrics.extraArgs String? None Additional arguments to be passed directly to the command.
collectVariantCallingMetrics.jobMemory Int 12 Memory allocated to job (in GB).
collectVariantCallingMetrics.overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
collectVariantCallingMetrics.cores Int 1 The number of cores to allocate to the job.
collectVariantCallingMetrics.timeout Int 24 Maximum amount of time (in hours) the task can run for.

Outputs

Output Type Description Labels
output_raw_vcf File Merged raw vcf
output_raw_vcf_index File Merged raw vcf index
detail_metrics_file File? The output detailed metrics report file
summary_metrics_file File? The output summary metrics report file.
output_recalibrated_vcf File? The output recalibrated VCF file in which each variant is annotated with its VQSLOD value
output_recalibrated_vcf_index File? The output recalibrated VCF index file

Commands

This section lists command(s) run by genotypegvcfs workflow

  • Running genotypegvcfs

Format intervals for parallel execution

     echo "~{intervalsToParallelizeBy}" | tr '~{lineSeparator}' '\n'

Run GenomicsDBImport

     set -euo pipefail
     mkdir -p ~{tmpDir}
 
     gatk --java-options -Xmx~{jobMemory - overhead}G \
       GenomicsDBImport \
       --genomicsdb-workspace-path ~{workspace_dir_name} \
       -V ~{sep=" -V " vcfs} \
       -L ~{interval} \
       --tmp-dir=~{tmpDir} \
       ~{extraArgs}
 
       tar -cf ~{workspace_dir_name}.tar ~{workspace_dir_name}

Running GenotypeGVCFs

     set -euo pipefail
 
     tar -xf ~{workspace_tar}
     WORKSPACE=$(basename ~{workspace_tar} .tar)
 
     gatk --java-options -Xmx~{jobMemory - overhead}G \
       GenotypeGVCFs \
       -R ~{refFasta} \
       -V gendb://$WORKSPACE \
       -L ~{interval} \
       -D ~{dbsnpFilePath} \
       -stand-call-conf ~{standCallConf}  \
       -O "~{outputName}" \
       ~{extraArgs}

GatherVcfs

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" GatherVcfs \
     -I ~{sep=" -I " vcfs} \
     -O ~{outputFileNamePrefix}.raw.vcf.gz \
     ~{extraArgs}
 
     tabix -p vcf ~{outputFileNamePrefix}.raw.vcf.gz

VariantFiltration

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       VariantFiltration \
       --filter-expression "ExcessHet > ~{excess_het_threshold}" \
       --filter-name ExcessHet ~{extraArgs} \
       -O ~{outputFileNamePrefix}.excesshet.vcf.gz \
       -V ~{inputVcf}

MakeSitesOnlyVcf

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       MakeSitesOnlyVcf \
       -I ~{inputVcf} ~{extraArgs} \
       -O ~{outputFileNamePrefix}.sitesonly.vcf.gz

VariantRecalibrator

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       VariantRecalibrator \
       -V ~{inputVcf} \
       --trust-all-polymorphic \
       -tranche ~{sep=' -tranche ' recalibration_tranche_values} \
       -an ~{sep=' -an ' recalibration_annotation_values} \
       -mode INDEL \
       --max-gaussians ~{max_gaussians} \
       -resource:mills,known=false,training=true,truth=true,prior=12 ~{mills_vcf} \
       -resource:axiomPoly,known=false,training=true,truth=false,prior=10 ~{axiomPoly_vcf} \
       -resource:dbsnp,known=true,training=false,truth=false,prior=2 ~{dbsnp_vcf} \
       ~{extraArgs} -O ~{outputFileNamePrefix}.indels.recal \
       --tranches-file ~{outputFileNamePrefix}.indels.tranches

VariantRecalibrator

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       VariantRecalibrator \
       -V ~{inputVcf} \
       --trust-all-polymorphic \
       -tranche ~{sep=' -tranche ' recalibration_tranche_values} \
       -an ~{sep=' -an ' recalibration_annotation_values} \
       -mode SNP \
       --max-gaussians ~{max_gaussians} \
       -resource:hapmap,known=false,training=true,truth=true,prior=15 ~{hapmap_vcf} \
       -resource:omni,known=false,training=true,truth=true,prior=12 ~{omni_vcf} \
       -resource:1000G,known=false,training=true,truth=false,prior=10 ~{one_thousand_genomes_vcf} \
       -resource:dbsnp,known=true,training=false,truth=false,prior=7 ~{dbsnp_vcf} \
       ~{extraArgs} -O ~{outputFileNamePrefix}.snps.recal \
       --tranches-file ~{outputFileNamePrefix}.snps.tranches

ApplyVQSR

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       ApplyVQSR \
       -V ~{inputVcf} \
       --recal-file ~{indels_recalibration} \
       --tranches-file ~{indels_tranches} \
       --truth-sensitivity-filter-level ~{indel_filter_level} \
       --create-output-variant-index true \
       -mode INDEL ~{extraArgsIndel} \
       -O ~{outputFileNamePrefix}.indels.recalibrated.vcf.gz \
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       ApplyVQSR \
       -V ~{outputFileNamePrefix}.indels.recalibrated.vcf.gz \
       --recal-file ~{snps_recalibration} \
       --tranches-file ~{snps_tranches} \
       --truth-sensitivity-filter-level ~{snp_filter_level} \
       --create-output-variant-index true \
       -mode SNP ~{extraArgsSNP} \
       -O ~{outputFileNamePrefix}.indels.snps.recalibrated.vcf.gz \

CollectVariantCallingMetrics

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" \
       CollectVariantCallingMetrics \
       --INPUT ~{inputVcf} \
       --DBSNP ~{dbsnp_vcf} \
       --SEQUENCE_DICTIONARY ~{ref_dict} ~{extraArgs} \
       --OUTPUT ~{outputFileNamePrefix}

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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Genotype GVCFs WDL workflow for GATK4

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