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

Mutect2 missing variant

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    Bhanu Gandham

    Hi Enrico Cocchi

    Can you try the latest version of GATK v4.1.7.0 and let us know if you are still facing the same issue.

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    Enrico Cocchi

    I'll try it tomorrow, but do you guys know why is this happening?

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    David Benjamin

    Your output VCF shows that the variant at 33329989 is phased with another at 33329962.  This means that when your interval ends at 33329974 the variant haplotype has not rejoined the reference haplotype and our assembly engine sometimes has problems with this situation.  We are working on solutions to this issue.

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