CopywriteR: DNA copy number detection from off-target sequence data.
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ABSTRACT:
SUBMITTER: Kuilman T
PROVIDER: S-EPMC4396974 | biostudies-literature | 2015 Feb
REPOSITORIES: biostudies-literature
Publications
CopywriteR: DNA copy number detection from off-target sequence data.
Kuilman Thomas T Velds Arno A Kemper Kristel K Ranzani Marco M Bombardelli Lorenzo L Hoogstraat Marlous M Nevedomskaya Ekaterina E Xu Guotai G de Ruiter Julian J Lolkema Martijn P MP Ylstra Bauke B Jonkers Jos J Rottenberg Sven S Wessels Lodewyk F LF Adams David J DJ Peeper Daniel S DS Krijgsman Oscar O
Genome biology 20150227
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without referenc ...[more]
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