BioWDL: somatic-variantcalling

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This workflow uses several programs to call somatic variants and aggregate the results.

• strelka
• mutect2
• vardict
• manta
• somaticseq

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 somatic-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. For an overview of all available inputs, see this page.

{
  "SomaticVariantcalling.tumorBam": "The bam file to be processed",
  "SomaticVariantcalling.tumorBamIndex": "The bam file's index",
  "SomaticVariantcalling.tumorSample": "Name of the sample. This name will be used as a basename for the outputs.",
  "SomaticVariantcalling.referenceFasta": "A reference fasta file",
  "SomaticVariantcalling.referenceFastaFai": "The index for the reference fasta",
  "SomaticVariantcalling.referenceFastaDict": "The dict file for the reference fasta"
}

Some additional inputs that may be of interest are:

{
  "SomaticVariantcalling.controlBam": "A control (not tumor) sample bam file",
  "SomaticVariantcalling.controlBamIndex": "Index of the control bam file",
  "SomaticVariantcalling.controlSample": "Name of the control sample. Used as a basename for the outputs.",
  "SomaticVariantcalling.trainingSet": "A training set for SomaticSeq",
  "SomaticVariantcalling.runCombineVariants": "A boolean that notes whether the variant vcfs should be combined."
}

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 GatkPreprocess.outputDir. GatkPreprocess.outputDir must be mounted in the docker container. Cromwell will need a custom configuration to allow this.

Example

{
  "SomaticVariantcalling.tumorSample": "wgs3",
  "SomaticVariantcalling.tumorBam": "tests/data/wgs3/wgs3.bam",
  "SomaticVariantcalling.tumorBamIndex": "tests/data/wgs3/wgs3.bai",
  "SomaticVariantcalling.referenceFasta": "tests/data/reference/reference.fasta",
  "SomaticVariantcalling.referenceFastaFai": "tests/data/reference/reference.fasta.fai",
  "SomaticVariantcalling.referenceFastaDict": "tests/data/reference/reference.dict",
  "SomaticVariantcalling.trainingSet": {
    "truthIndel": "tests/data/wgs3/wgs3_indel_subset.vcf.gz",
    "truthSNV": "tests/data/wgs3/wgs3_snv_subset.vcf.gz",
    "tumorBam": "tests/data/wgs3/wgs3.bam",
    "tumorBamIndex": "tests/data/wgs3/wgs3.bai",
    "mutect2VCF": "tests/data/wgs3/somatic_variantcalling_vcfs/paired/mutect2/wgs3-wgs1.vcf.gz",
    "vardictVCF": "tests/data/wgs3/somatic_variantcalling_vcfs/paired/vardict/wgs3-wgs1.vcf.gz",
    "strelkaSNV": "tests/data/wgs3/somatic_variantcalling_vcfs/paired/strelka/strelka_variants.vcf.gz"
  },
  "SomaticVariantcalling.runCombineVariants": true
}

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

VCF files for each of the variant callers and a combined variants file.

Contact

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