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.
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| http://dx.doi.org/10.1093/bioinformatics/btx618 | DOI Listing |
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Canvas SPW: calling de novo copy number variants in pedigrees.
Bioinformatics
February 2018
Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10?1XL, UK.
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.
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