Workflows used for germline short variant discovery in WGS data

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

• GATK 4.0.10.1
• 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

• 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 https://github.com/openwdl/wdl/blob/master/LICENSE). 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.

• GATK
• BWA
• Picard
• Samtools