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Calling Somatic SNVs and Indels with Mutect2

David Benjamin, Takuto Sato, Kristian Cibulskis, Gad Getz, Chip Stewart, Lee Lichtenstein
doi: https://doi.org/10.1101/861054
David Benjamin
The Broad Institute, 415 Main Street, 02142 Cambridge, MA, USA
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  • For correspondence: davidben@broadinstitute.org
Takuto Sato
The Broad Institute, 415 Main Street, 02142 Cambridge, MA, USA
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Kristian Cibulskis
The Broad Institute, 415 Main Street, 02142 Cambridge, MA, USA
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Gad Getz
The Broad Institute, 415 Main Street, 02142 Cambridge, MA, USA
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Chip Stewart
The Broad Institute, 415 Main Street, 02142 Cambridge, MA, USA
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Lee Lichtenstein
The Broad Institute, 415 Main Street, 02142 Cambridge, MA, USA
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Abstract

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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted December 02, 2019.
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Calling Somatic SNVs and Indels with Mutect2
David Benjamin, Takuto Sato, Kristian Cibulskis, Gad Getz, Chip Stewart, Lee Lichtenstein
bioRxiv 861054; doi: https://doi.org/10.1101/861054
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Calling Somatic SNVs and Indels with Mutect2
David Benjamin, Takuto Sato, Kristian Cibulskis, Gad Getz, Chip Stewart, Lee Lichtenstein
bioRxiv 861054; doi: https://doi.org/10.1101/861054

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