Canvas SPW: calling de novo copy number variants in pedigrees

Abstract 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. Supplementary information Supplementary data are available at Bioinformatics online.