deepSNV

Detection of subclonal SNVs in deep sequencing data.

Bioconductor version: 3.24 · Package version: 1.59.0

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("deepSNV")