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This repository has been archived by the owner on May 13, 2020. It is now read-only.

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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gatk-workflows/gatk4-mitochondria-pipeline

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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 :

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.

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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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