Canvas SPW: calling de novo copy number variants in pedigrees
- Resource Type
- Authors
- Sergii Ivakhno; Anthony J. Cox; Camilla Colombo; Eric Roller; Philip Tedder
- Source
- Bioinformatics (Oxford, England). 34(3)
- Subject
- 0301 basic medicine
Statistics and Probability
DNA Copy Number Variations
Computer science
Sequence analysis
Sequencing data
Pedigree chart
Computational biology
Biology
Biochemistry
03 medical and health sciences
0302 clinical medicine
Humans
Copy-number variation
Molecular Biology
Genetics
Whole genome sequencing
Breakpoint
Genomics
Sequence Analysis, DNA
Computer Science Applications
Pedigree
Computational Mathematics
Identification (information)
030104 developmental biology
Computational Theory and Mathematics
Identification (biology)
030217 neurology & neurosurgery
Software
- Language
- ISSN
- 1367-4811
MotivationWhole 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.ResultsWe 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.AvailabilityCanvas SPW is available for download from https://github.com/Illumina/canvas.Contactsivakhno@illumina.comSupplementary informationSupplementary data are available at Bioinformatics online.