Workflows for validating sequence data

This WDL performs format validation on SAM/BAM files in a list

• One or more SAM or BAM files to validate
• Explicit request of either SUMMARY or VERBOSE mode in inputs.json

• Set of .txt files containing the validation reports, one per input file

• Successfully tested on v49
• Does not work on versions < v23 due to output syntax

• 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.

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.