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

Calling somatic multi-nucleotide polymorphisms with Mutect2

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    David Benjamin

    There are no settings to do that.  Mutect2 defines alleles relative to the reference.  In the future we do want to be more sophisticated and do things like call the tumor relative to an assembly of the normal.

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    Dilys Weijers

    Thank you for your quick response. Then, as a follow-up, is it possible to output SNPs and Indels only, so we can call the MNPs from the list of SNPs ourselves with a seperate tool?

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    David Benjamin

    Yes, the setting -max-mnp-distance 0 turns off MNP calling.

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