PT  - JOURNAL ARTICLE
AU  - Benjamin, David
AU  - Sato, Takuto
AU  - Cibulskis, Kristian
AU  - Getz, Gad
AU  - Stewart, Chip
AU  - Lichtenstein, Lee
TI  - Calling Somatic SNVs and Indels with Mutect2
AID  - 10.1101/861054
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 861054
4099  - http://biorxiv.org/content/early/2019/12/02/861054.short
4100  - http://biorxiv.org/content/early/2019/12/02/861054.full
AB  - 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.