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Samovar: Single-sample mosaic SNV calling with linked reads

By Charlotte Darby, James R Fitch, Patrick J. Brennan, Benjamin J Kelly, Natalie Bir, Vincent Magrini, Jeffrey Leonard, Catherine E Cottrell, Julie M Gastier-Foster, Richard K Wilson, Elaine R. Mardis, Peter White, Ben Langmead, Michael C. Schatz

Posted 25 Feb 2019
bioRxiv DOI: 10.1101/560532 (published DOI: 10.1016/j.isci.2019.05.037)

We present Samovar, a mosaic single-nucleotide variant (SNV) caller for linked-read whole-genome shotgun sequencing data. Samovar scores candidate sites using a random forest model trained using the input dataset that considers read quality, phasing, and linked-read characteristics. We show Samovar calls mosaic SNVs within a single sample with accuracy comparable to what previously required trios or matched tumor/normal pairs and outperform single-sample mosaic variant callers at MAF 5%-50% with at least 30x coverage. Furthermore, we use Samovar to find somatic variants in whole genome sequencing of both tumor and normal from 13 pediatric cancer cases that can be corroborated with high recall with whole exome sequencing. Samovar is available open-source at https://github.com/cdarby/samovar under the MIT license.

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