recipe bioconductor-deepsnv

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/deepSNV.html

License

GPL-3

Recipe

/bioconductor-deepsnv/meta.yaml

Links

biotools: deepsnv

package bioconductor-deepsnv

(downloads) docker_bioconductor-deepsnv

Versions

1.30.0-1, 1.28.0-0, 1.26.1-0, 1.24.0-0, 1.22.0-0, 1.20.0-0

Depends
Required By

Installation

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

conda install bioconductor-deepsnv

and update with:

conda update bioconductor-deepsnv

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-deepsnv:<tag>

(see bioconductor-deepsnv/tags for valid values for <tag>)