mitochondria-pipeline

Purpose :

Workflow for SNP and INDEL variant calling on mitochondria.

Requirements/expectations :

• BAM or CRAM file
• Median of the coverage over the autosome (if available, another central statistic would work too)
• Reference fasta (along with its index and dictionary) is only required when input is a BAM
• Default for max_read_length is 151, this is purely an optimization parameter and won't effect the results.

Output :

• A VCF file and its index
• Addtional Metrics
• Optional realigned to chrM BAM

Software version notes :

• GATK 4.1
• Cromwell version support
  • Successfully tested on v37
  • Does not work on versions < v23 due to output syntax

Important Notes :

• 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.
• 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.

Contact Us :

• 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.

LICENSING :

Copyright Broad Institute, 2020 | 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.