bioconda / packages / bioconductor-deepsnv 1.34.0

Detection of subclonal SNVs in deep sequencing data.

Installers

Info: This package contains files in non-standard labels.

conda install

  • linux-64  v1.34.0
  • osx-64  v1.34.0
To install this package with conda run one of the following:
conda install -c bioconda bioconductor-deepsnv
conda install -c bioconda/label/gcc7 bioconductor-deepsnv
conda install -c bioconda/label/cf201901 bioconductor-deepsnv

Description

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.

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