gatk4-mitochondria-pipeline

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gatk4-mitochondria-pipeline

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This repo is be archived, these workflows are still housed housed in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.

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# 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](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591) 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](https://gatk.broadinstitute.org/hc/en-us/articles/360035530952).
- Please visit the [User Guide](https://gatk.broadinstitute.org/hc/en-us/categories/360002310591) site for further documentation on our workflows and tools.
- Relevant reference and resources bundles can be accessed in [Resource Bundle](https://gatk.broadinstitute.org/hc/en-us/articles/360036212652).

### 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](https://gatk.broadinstitute.org/hc/en-us/community/topics) or [Terra](https://support.terra.bio/hc/en-us/community/topics/360000500432).

### 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.

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