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.
|Author||Niko Beerenwinkel [ths], David Jones [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]|
|Bioconductor views||DataImport GeneticVariability Genetics SNP Sequencing|
|Maintainer||Moritz Gerstung <email@example.com>|
|Package repository||View on Bioconductor|
Install the latest version of this package by entering the following in R:
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.