haplotypeCaller

Workflow to run the GATK Haplotype Caller

Overview

Dependencies

• GATK4

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
bai	File	The index for the BAM file to be used.
bam	File	The BAM file to be used.
reference	String	Assembly id, i.e. hg38
intervalsToParallelizeBy	String	Comma separated list of intervals to split by (e.g. chr1,chr2,chr3,chr4).
mergeGVCFs.modules	String	Required environment modules.

Optional workflow parameters:

Parameter	Value	Default	Description
filterIntervals	String?	None	Path to a BED file that restricts calling to only the regions in the file.
outputFileNamePrefix	String	basename(bam,".bam")	Prefix for output file.
rnaMode	Boolean	false	flag to indicate whether to run RNA sequencing data. Default is false (DNA mode).
GVCF	Boolean	true	flag to indicated whether the output is VCF or GVCF (default).

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.
callHaplotypes.extraArgs	String?	None	Additional arguments to be passed directly to the command.
callHaplotypes.intervalPadding	Int	100	The number of bases of padding to add to each interval.
callHaplotypes.intervalSetRule	String	"INTERSECTION"	Set merging approach to use for combining interval inputs.
callHaplotypes.jobMemory	Int	24	Memory allocated to job (in GB).
callHaplotypes.overhead	Int	6	Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
callHaplotypes.cores	Int	1	The number of cores to allocate to the job.
callHaplotypes.timeout	Int	72	Maximum amount of time (in hours) the task can run for.
mergeGVCFs.jobMemory	Int	24	Memory allocated to job (in GB).
mergeGVCFs.overhead	Int	6	Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
mergeGVCFs.cores	Int	1	The number of cores to allocate to the job.
mergeGVCFs.timeout	Int	24	Maximum amount of time (in hours) the task can run for.

Outputs

Output	Type	Description	Labels
outputVcf	File	output vcf	vidarr_label: outputVcf
outputVcfIndex	File	output vcf index	vidarr_label: outputVcfIndex

Commands

This section lists commands run by haplotypeCaller workflow

• Running haplotypeCaller

Workflow to run the GATK Haplotype Caller

Parsing intervals

    echo INTERVALS_TO_PARALLELIZE_BY | tr 'LINE_SEPARATOR' '\n'

Running haplotypeCaller DNA mode

    set -euo pipefail

    gatk --java-options -Xmx[JOB_MEMORY - OVERHEAD]G HaplotypeCaller \
    -R REFERENCE_FASTA \
    -I INPUT_BAM \
    -L INTERVAL_FILE \
    -L FILTER_INTERVALS -isr INTERVAL_SetRule -ip INTERVAL_Padding \ # Optional
    -D DBSNP_VCF \
    -ERC ERC \
    --EXTRA_ARGUMENTS \
    -O OUTPUT \

Running haplotypeCaller RNA mode

    set -euo pipefail

    gatk --java-options -Xmx[JOB_MEMORY - OVERHEAD]G HaplotypeCaller \
    -R REFERENCE_FASTA \
    -I INPUT_BAM \
    -L INTERVAL_FILE \
    -L FILTER_INTERVALS -isr INTERVAL_SetRule -ip INTERVAL_Padding \ # Optional
    -D DBSNP_VCF \
    -ERC ERC \
    --dont-use-soft-clipped-bases \
    --standard-min-confidence-threshold-for-calling 20 \
    --max-reads-per-alignment-start 0 \
    -G StandardAnnotation \
    -G StandardHCAnnotation \
    --EXTRA_ARGUMENTS \
    -O OUTPUT \

Merging vcf files

    set -euo pipefail

    gatk --java-options "-Xmx[JOB_MEMORY - OVERHEAD]G" MergeVcfs
    -I VCF_FILES
    -O OUTPUT

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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