BioWDL: gatk-variantcalling

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This workflow can be used to generate a multisample VCF file from BAM files using GATK HaplotypeCaller.

This workflow is part of BioWDL developed by the SASC team at Leiden University Medical Center.

Usage

This workflow can be run using Cromwell:

java -jar cromwell-<version>.jar run -i inputs.json gatk-variantcalling.wdl

Inputs

Inputs are provided through a JSON file. The minimally required inputs are described below and a template containing all possible inputs can be generated using Womtool as described in the WOMtool documentation.

{
  "GatkVariantCalling.referenceFasta": "A reference fasta file",
  "GatkVariantCalling.referenceFastaFai": "The index for the reference fasta",
  "GatkVariantCalling.referenceFastaDict": "The dict file for the reference fasta",
  "GatkVariantCalling.dbsnpVCF": "A dbSNP VCF file",
  "GatkVariantCalling.dbsnpVCFIndex": "The index (.tbi) for the dbSNP VCF file",
  "GatkVariantCalling.bamFiles": "A list of input BAM files and their associated indexes"
}

Some additional inputs which may be of interest are:

{
  "GatkVariantCalling.scatterList.regions": "The path to a bed file containing the regions for which variant calling will be performed",
  "GatkVariantCalling.scatterSize": "The size of scatter regions (see explanation of scattering below), defaults to 10,000,000",
  "GatkVariantCalling.vcfBasename": "The basename of the to be outputed VCF files, defaults to 'multisample'"
}

An output directory can be set using an options.json file. See the cromwell documentation for more information.

Example options.json file:

{
"final_workflow_outputs_dir": "my-analysis-output",
"use_relative_output_paths": true,
"default_runtime_attributes": {
  "docker_user": "$EUID"
  }
}

Alternatively an output directory can be set with GatkVariantCalling.outputDir. GatkVariantCalling.outputDir must be mounted in the docker container. Cromwell will need a custom configuration to allow this.

Example

{
  "GatkVariantCalling.dbsnpVCF": "/home/user/genomes/human/dbsnp/dbsnp-151.vcf.gz",
  "GatkVariantCalling.dbsnpVCFIndex": "/home/user/genomes/human/dbsnp/dbsnp-151.vcf.gz.tbi",
  "GatkVariantCalling.referenceFasta": "/home/user/genomes/human/GRCh38.fasta",
  "GatkVariantCalling.referenceFastaFai": "/home/user/genomes/human/GRCh38.fasta.fai",
  "GatkVariantCalling.referenceFastaDict": "/home/user/genomes/human/GRCh38.dict",
  "GatkVariantCalling.vcfBasename": "s1",
  "GatkVariantCalling.outputDir": "/home/user/analysis/results/",
  "GatkVariantCalling.bamFiles": [
    {
      "file": "/home/user/mapping/results/s1_1.bam",
      "index": "/home/user/mapping/results/s1_1.bai"
    },
    {
      "file": "/home/user/mapping/results/s1_2.bam",
      "index": "/home/user/mapping/results/s1_2.bai"
    }
  ]
}

Dependency requirements and tool versions

Biowdl pipelines use docker images to ensure reproducibility. This means that biowdl pipelines will run on any system that has docker installed. Alternatively they can be run with singularity.

For more advanced configuration of docker or singularity please check the cromwell documentation on containers.

Images from biocontainers are preferred for biowdl pipelines. The list of default images for this pipeline can be found in the default for the dockerImages input.

output

A multisample vcf file and a multisample gvcf file.

Scattering

This pipeline performs scattering to speed up analysis on grid computing clusters. This is done by splitting the reference genome into regions of roughly equal size (see the scatterSize input). Each of these regions will be analyzed in separate jobs, allowing them to be processed in parallel.

For each BAM file input in the pipeline these scatters will be used. For example, with 5 BAM files and 4 scatters, 20 jobs will run to genotype the BAM files. The resulting GVCF files will be merged. Then GatkGenotypeGVCF will be scattered over the 4 scatters to create a VCF per scatters. The output is merged into a multisample vcf.

Contact

For any question related to this workflow, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.