BioWDL: bam-to-gvcf

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

This workflow is part of BioWDL developed by the SASC team.

Usage

This workflow can be run using Cromwell:

java -jar cromwell-<version>.jar run -i inputs.json gvcf.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. See this page for some additional general notes and information about pipeline inputs.

{
  "Gvcf.dbsnpVCF": {
    "file": "A dbSNP VCF file",
    "index": "The index (.tbi) for the dbSNP VCF file"
  },
  "Gvcf.reference": {
    "fasta": "A reference fasta file",
    "fai": "The index for the reference fasta",
    "dict": "The dict file for the reference fasta"
  },
  "Gvcf.gvcfPath": "The path the output GVCF file will be written to",
  "Gvcf.bamFiles": "A list of input BAM files and their associated indexes"
}

Some additional inputs which may be of interest are:

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

Example

{
  "Gvcf.dbsnpVCF": {
    "file": "/home/user/genomes/human/dbsnp/dbsnp-151.vcf.gz",
    "index": "/home/user/genomes/human/dbsnp/dbsnp-151.vcf.gz.tbi"
  },
  "Gvcf.reference": {
    "fasta": "/home/user/genomes/human/GRCh38.fasta",
    "fai": "/home/user/genomes/human/GRCh38.fasta.fai",
    "dict": "/home/user/genomes/human/GRCh38.dict"
  },
  "Gvcf.gvcfPath": "/home/user/analysis/results/s1.vcf.gz",
  "Gvcf.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

Included in the repository is an environment.yml file. This file includes all the tool version on which the workflow was tested. You can use conda and this file to create an environment with all the correct tools.

output

A GVCF file at the specified location and its index.

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.

Contact

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