bioconductor-deepsnv

downloads

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.

Home http://bioconductor.org/packages/3.6/bioc/html/deepSNV.html
Versions 1.20.0, 1.22.0, 1.24.0
License GPL-3
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-deepsnv

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-deepsnv

and update with:

conda update bioconductor-deepsnv

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-deepsnv.