Workflows for germline short variant discovery with GATK4.

The haplotypecaller-gvcf-gatk4 workflow runs the GATK4 HaplotypeCaller tool in GVCF mode on a single sample according to GATK Best Practices. When executed the workflow scatters the HaplotypeCaller tool over the input bam sample using an interval list file. The output produced by the workflow will be a single GVCF file which can then be provided to GenomicsDBImport along with several other GVCF files to call for variants simultaneously, producing a multisample VCF. The haplotypecaller-gvcf-gatk4 workflows default GVCF mode is useful when calling variants for several samples efficiently. However, for instances when calling variants for one or a few samples it is possible to have the workflow directly call variants and output a VCF file by setting the make_gvcf input variable to false.

• One analysis-ready BAM file for a single sample (as identified in RG:SM)
• A file containing a set of variant calling interval list for the scatter

• One GVCF file and its index

• GATK 4
• Samtools 1.3.1
• Python 2.7
• Cromwell version support
  • Successfully tested on v53

• The JointGenotyping workflow takes the GVCF output produced by the haplotypecaller-gvcf-gatk and uses GenomicsDBImport to produce a multi-sample VCF. The JointGenotyping workflow requires GVCFs be listed in a sample map text file, this can be generated using the generate-sample-map workflow.
• The provided JSON is 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.
• 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.
• Please visit the User Guide site for further documentation on our workflows and tools.
• Relevant reference and resources bundles can be accessed in Resource Bundle.

• The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : GATK or Terra.

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
• Samtools