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

VariantFilteration and Selectvariant (Mitochondrial mode) - Missing True Positive Variants


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    David Benjamin

    Jyoti Mridha This looks like a custom-made filtering pipeline.  It does not resemble our best practices.  The hard filtering most likely does very little since it is filtering based on several annotations -- QUAL, QD, ReadPosRankSum, MQRankSum -- that Mutect2 does not emit.

    Our recommendation is simply to run Mutect2 and FilterMutectCalls in mitochondria mode with default options.

    Finally, the zygosity emitted by Mutect2 is meaningless.  The VCF spec assumes an integer ploidy which is not appropriate for aneuploidy and heteroplasmy such as occurs in cancer and mitochondria.  A 0/1 genotype just means that a variant exists, which is totally redundant.

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