Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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


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    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.


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    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)? 



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    Is this pipeline specific to human, or can it be used for other species such as mus musculus?


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    Solenne Correard

    Hi team!

    Thanks for this. I am using gatk4-4.2.0 and it seems like two flags are no longer supported :

    --median-autosomal-coverage (CallMt step using Mutect2)

    A USER ERROR has occurred: median-autosomal-coverage is not a recognized option

    --autosomal-coverage (Filter the variant by parameter step using FilterMutectCalls)

    A USER ERROR has occurred: autosomal-coverage is not a recognized option

    They are not mentioned in the updates with the newer releases of GATK4. Will they be included in future release or should the best practices be updated? Thanks a lot for everything!


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