Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mitochondrial short variant discovery (SNVs + Indels) Follow


  • Avatar
    Troy LoBue

    Is this pipeline for germline mutation calling or only somatic? What is the best way to call variants in the mitochondrial genome with whole genome data? Thank you in advance.


    Comment actions Permalink
  • Avatar
    Yao Yao

    Hi GATK team, Thanks for generating this pipeline. I am wondering is this pipeline suitable for WES data which included the mitochondrial reads coverage(probe)? 



    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk