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This is the development version of deepSNV; for the stable release version, see deepSNV.

Detection of subclonal SNVs in deep sequencing data.

Bioconductor version: Development (3.20)

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], Raul Alcantara [ctb], David Jones [ctb], John Marshall [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]

Maintainer: Moritz Gerstung <moritz.gerstung at>

Citation (from within R, enter citation("deepSNV")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

An R package for detecting low frequency variants in deep sequencing experiments PDF R Script
Shearwater ML HTML R Script
Subclonal variant calling with multiple samples and prior knowledge using shearwater PDF R Script
Reference Manual PDF


biocViews DataImport, GeneticVariability, Genetics, SNP, Sequencing, Software
Version 1.51.0
In Bioconductor since BioC 2.10 (R-2.15) (12.5 years)
License GPL-3
Depends R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation(>= 1.27.6)
Imports Rhtslib
System Requirements GNU make
See More
Suggests RColorBrewer, knitr, rmarkdown
Linking To Rhtslib(>= 1.13.1)
Depends On Me
Imports Me mitoClone2
Suggests Me GenomicFiles
Links To Me
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Source Package deepSNV_1.51.0.tar.gz
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macOS Binary (arm64) deepSNV_1.51.0.tgz
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