isma: an R package for the integrative analysis of mutations detected by multiple pipelines

BMC Bioinformatics
Noemi Di NanniEttore Mosca

Abstract

Recent comparative studies have brought to our attention how somatic mutation detection from next-generation sequencing data is still an open issue in bioinformatics, because different pipelines result in a low consensus. In this context, it is suggested to integrate results from multiple calling tools, but this operation is not trivial and the burden of merging, comparing, filtering and explaining the results demands appropriate software. We developed isma (integrative somatic mutation analysis), an R package for the integrative analysis of somatic mutations detected by multiple pipelines for matched tumor-normal samples. The package provides a series of functions to quantify the consensus, estimate the variability, underline outliers, integrate evidences from publicly available mutation catalogues and filter sites. We illustrate the capabilities of isma analysing breast cancer somatic mutations generated by The Cancer Genome Atlas (TCGA) using four pipelines. Comparing different "points of view" on the same data, isma generates a unique mutation catalogue and a series of reports that underline common patterns, variability, as well as sites already catalogued by other studies (e.g. TCGA), so as to design and apply filtering st...Continue Reading

References

Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
May 15, 2012·Bioinformatics·Christopher T SaundersR Keira Cheetham
Feb 12, 2013·Nature Biotechnology·Kristian CibulskisGad Getz
Jul 12, 2013·Bioinformatics·Nicola D RobertsDavid L Adelson
Dec 26, 2015·Nucleic Acids Research·Antonio ColapricoHoutan Noushmehr
Jul 13, 2016·Molecular Ecology Resources·Brian J Knaus, Niklaus J Grünwald
Oct 14, 2017·Bioinformatics·Michael Lawrence, Robert Gentleman
Oct 17, 2017·Bioinformatics·Alessandro Pietrelli, Luca Valenti

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Citations

Sep 11, 2019·Bioinformatics·Noemi Di NanniEttore Mosca

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Software Mentioned

BAYSIC
varscan
isma
R
vcfR
VCFTools
Cake
pipe
VariantTools
R package

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