deepSNV is an R package for calling subclonal single-nucleotide variants from paired deep sequencing experiments.This package provides provides a quantitative variant caller for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. It assumes a comparative setup with a control experiment of the same loci and a beta-binomial model to discriminate sequencing errors and subclonal SNVs.
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Nat Commun. 2012 May 1;3:811. doi: 10.1038/ncomms1814.
Reliable detection of subclonal single-nucleotide variants in tumour cell populations.
Gerstung M1, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N.