recipe bioconductor-deepsnv

Detection of subclonal SNVs in deep sequencing data.

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/deepSNV.html

License:

GPL-3

Recipe:

/bioconductor-deepsnv/meta.yaml

Links:

biotools: 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.

package bioconductor-deepsnv

(downloads) docker_bioconductor-deepsnv

Versions:
1.44.0-01.40.0-21.40.0-11.40.0-01.38.0-01.36.0-11.36.0-01.34.0-01.32.0-0

1.44.0-01.40.0-21.40.0-11.40.0-01.38.0-01.36.0-11.36.0-01.34.0-01.32.0-01.30.0-11.28.0-01.26.1-01.24.0-01.22.0-01.20.0-0

Depends:
Required By:

Installation

With an activated Bioconda channel (see 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>)

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