deepSNV-package: Detection of subclonal SNVs in deep sequencing experiments

In deepSNV: Detection of subclonal SNVs in deep sequencing data.

Description

Detection of subclonal SNVs in deep sequencing experiments

Details

This packages provides algorithms for detecting subclonal single nucleotide variants (SNVs) and their frequencies from ultra-deep sequencing data. It retrieves the nucleotide counts at each position and each strand from two .bam files and tests for differences between the two experiments with a likelihood ratio test using either a binomial or and overdispersed beta-binomial model. The statistic can be tuned across genomic sites by a shared Dirichlet prior and there package provides procedures for normalizing sequencing data from different runs.

Author(s)

Moritz Gerstung, Wellcome Trust Sanger Institute, [e-mail]

References

Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, and Beerenwinkel N. Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat Commun 3:811 (2012). DOI:10.1038/ncomms1814.

See Also

deepSNV

Examples

## Short example with 2 SNVs at frequency ~10%
regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140)
ex <- deepSNV(test = system.file("extdata", "test.bam", package="deepSNV"), control = system.file("extdata", "control.bam", package="deepSNV"), regions=regions, q=10)
show(ex)   # show method
plot(ex)   # scatter plot
summary(ex)   # summary with significant SNVs
ex[1:3,]   # subsetting the first three genomic positions
tail(test(ex, total=TRUE))   # retrieve the test counts on both strands
tail(control(ex, total=TRUE))

## Not run: Full example with ~ 100 SNVs. Requires an internet connection, but try yourself.
# regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585)
# HIVmix <- deepSNV(test = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", control = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam", regions=regions, q=10)
data(HIVmix) # attach data instead..
show(HIVmix)
plot(HIVmix)
head(summary(HIVmix))

deepSNV documentation built on Nov. 8, 2020, 8:01 p.m.