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.

Code

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Topics

Depended on by (2)

People

• Moritz Gerstung author maintainer
• Raul Alcantara contributor
• Niko Beerenwinkel ths
• David Jones contributor
• John Marshall contributor
• Inigo Martincorena contributor