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Calling Somatic SNVs and Indels with Mutect2

By David Benjamin, Takuto Sato, Kristian Cibulskis, Gad A. Getz, Chip Stewart, Lee Lichtenstein

Posted 02 Dec 2019
bioRxiv DOI: 10.1101/861054

Mutect2 is a somatic variant caller that uses local assembly and realignment to detect SNVs and indels. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling. Beyond local assembly and alignment, Mutect2 is based on several probabilistic models for genotyping and filtering that work well with and without a matched normal sample and for all sequencing depths.

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