Genome Biology · 2015 · 232 citations · 43 references
Life SciencesGeneticsMolecular GeneticsGenomic Data AnalysisGenomic InformaticsGenomicsCopy Number Variant AnalysisCopy Number VariantsCopy Number VariationDna SequencingNext-generation SequencingVariant DetectionCopy Number Alteration DetectionCopy Number ProfilingCopy Number Variant CallingCopy Number Variant DetectionCopy Number Variation DetectionNext-generation Sequencing Based Copy Number AnalysisNext-generation Sequencing Data AnalysisNext-generation Sequencing-based Copy Number Analysis
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 reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.
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An integrated encyclopedia of DNA elements in the human genome