Canvas SPW: Calling De Novo Copy Number Variants in Pedigrees.

Motivation:Whole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited and de novo copy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure.Results:We have developed a new tool, Canvas SPW, for the identification of inherited and de novo copy number variants from pedigree sequencing data. Canvas SPW supports a number of family structures and provides a wide range of scoring and filtering options to automate and streamline identification of de novo variants.Availability and implementation:Canvas SPW is available for download from https://github.com/Illumina/canvas.Contact:sivakhno@illumina.com.Supplementary information:Supplementary data are available at Bioinformatics online.