PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data

• DOI: 10.1093/bioinformatics/btu363
• Publication Date: 2014-05-30T02:31:57Z
• Authors: Chen Wang; Jared M. Evans; Aditya V. Bhagwate; Naresh Prodduturi; Vivekananda Sarangi; Mridu Middha; Hugues Sicotte; Peter T. Vedell; Steven N. Hart; Gavin R. Oliver; Jean-Pierre A. Ko...; Matthew J. Maurer; Anne J. Novak; Susan L. Slager; James R. Cerhan; Yan W. Asmann
• Keywords: Perl; Exome

Abstract Motivation: Exome sequencing (exome-seq) data, which are typically used for calling exonic mutations, have also been utilized in detecting DNA copy number variations (CNVs). Despite the existence of several CNV detection tools, there is still a great need sensitive and an accurate CNV-calling algorithm with built-in QC steps, does not require paired reference each sample. Results: We developed novel method named PatternCNV, (i) accounts read coverage between exons while leveraging consistencies this variability across different samples; (ii) reduces alignment BAM files to WIG format therefore greatly accelerates computation; (iii) incorporates multiple measures designed identify outlier samples batch effects; (iv) provides variety visualization options including chromosome, gene exon-level views CNVs, along tabular summarization CNVs. Compared other algorithms using data from lymphoma exome-seq study, PatternCNV has higher sensitivity specificity. Availability implementation: The software implemented Perl R, can be Mac or Linux environments. Software user manual available at http://bioinformaticstools.mayo.edu/research/patterncnv/ , R package https://github.com/topsoil/patternCNV/ . Contact: [e-mail] Supplementary information: Bioinformatics online.