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Workflows used for germline short variant discovery in WGS data

This repository has been deprecated in favor of

germline_single_sample_workflow :

This WDL pipeline implements data pre-processing and initial variant calling (GVCF generation) according to the GATK Best Practices (June 2016) for germline SNP and Indel discovery in human whole-genome sequencing data.


  • Human whole-genome paired-end sequencing data in unmapped BAM (uBAM) format
  • One or more read groups, one per uBAM file, all belonging to a single sample (SM)
  • Input uBAM files must additionally comply with the following requirements:
    • filenames all have the same suffix (we use ".unmapped.bam")
    • files must pass validation by ValidateSamFile
    • reads are provided in query-sorted order
    • all reads must have an RG tag
  • Reference genome must be Hg38 with ALT contigs


  • Cram, cram index, and cram md5
  • GVCF and its gvcf index
  • BQSR Report
  • Several Summary Metrics

Software version requirements :

  • GATK
  • Picard 2.16.0-SNAPSHOT
  • Samtools 1.3.1
  • Python 2.7
  • Cromwell version support
    • Successfully tested on v37
    • Does not work on versions < v23 due to output syntax

Important Note :

  • The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables using the GATK Tool and Tutorial Documentations.
  • Relevant reference and resources bundles can be accessed in Resource Bundle.
  • Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
  • For help running workflows on the Google Cloud Platform or locally please view the following tutorial (How to) Execute Workflows from the gatk-workflows Git Organization.
  • The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : GATK , FireCloud or Terra , WDL/Cromwell.
  • Please visit the User Guide site for further documentation on our workflows and tools.


Copyright Broad Institute, 2019 | BSD-3 This script is released under the WDL open source code license (BSD-3) (full license text at Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.