gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

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.

Getting started

Package details

Bioconductor views DataImport GeneticVariability Genetics SNP Sequencing
MaintainerMoritz Gerstung <[email protected]>
LicenseGPL-3
Version1.27.3
URL http://github.com/gerstung-lab/deepSNV
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("gerstung-lab/deepSNV")
gerstung-lab/deepSNV documentation built on Oct. 6, 2018, 9:13 a.m.