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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

Why no overlaps between shifted variants and non-shifted variants in gatk4-mitochondria-pipeline? (Mutect2)


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    Megan Shand

    Hi Changhan,

    Did you use the mitochondria best practices WDL? If so, then I'm not surprised that there are no overlapping variants in the two VCFs. We only call the control region of the mitochondria with the shifted reference and then only call the rest of the mitochondria with the regular reference. You can see this in the -L arguments of the WDL (it's chrM:576-16024 for the non-control region, everything else is considered the control region). 

    In the commands you posted through, it looks like you're only using -L chrM, so I'm not sure why there aren't overlapping sites in your vcfs if both were called across the entire mitochondria.

    I'm also not sure why you're seeing so many indels. It looks like you haven't run FilterMutectCalls yet (or the other filtering steps in the pipeline). Perhaps the filtering steps would remove false sites in your callset and the results would look more like what you expect.



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