Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

• uBAM

• A BAM file and its index.
• A VCF file and its index.
• A Filtered VCF file and its index.

Runtime parameters are optimized for Broad's Google Cloud Platform implementation. For program versions, see docker containers.

• Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
• The provided JSON is a ready to use example JSON template of the workflow. Users are responsible for reviewing the GATK Tool and Tutorial Documentations to properly set the reference and resource variables.
• 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.
• 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.

This script is released under the WDL source code license (BSD-3) (see LICENSE in https://github.com/broadinstitute/wdl). 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. Please see the docker page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed licensing information pertaining to the included programs.