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.
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.
Authors: Adeline Vanderver; Geneviève Bernard; Guy Helman; Omar Sherbini; Ryan Boeck; Jeffrey Cohn; Abigail Collins; Scott Demarest; Katherine Dobbins; Lisa Emrick; Jamie L Fraser; Diane Masser-Frye; Jean Hayward; Swati Karmarkar; Stephanie Keller; Samuel Mirrop; Wendy Mitchell; Sheel Pathak; Elliott Sherr; Keith van Haren; Erica Waters; Jenny L Wilson; Leah Zhorne; Raphael Schiffmann; Marjo S van der Knaap; Amy Pizzino; Holly Dubbs; Justine Shults; Cas Simons; Ryan J Taft Journal: Ann Neurol Date: 2020-06-09 Impact factor: 10.422
Authors: Ann E Frazier; Alison G Compton; Yoshihito Kishita; Daniella H Hock; AnneMarie E Welch; Sumudu S C Amarasekera; Rocio Rius; Luke E Formosa; Atsuko Imai-Okazaki; David Francis; Min Wang; Nicole J Lake; Simone Tregoning; Jafar S Jabbari; Alexis Lucattini; Kazuhiro R Nitta; Akira Ohtake; Kei Murayama; David J Amor; George McGillivray; Flora Y Wong; Marjo S van der Knaap; R Jeroen Vermeulen; Esko J Wiltshire; Janice M Fletcher; Barry Lewis; Gareth Baynam; Carolyn Ellaway; Shanti Balasubramaniam; Kaustuv Bhattacharya; Mary-Louise Freckmann; Susan Arbuckle; Michael Rodriguez; Ryan J Taft; Simon Sadedin; Mark J Cowley; André E Minoche; Sarah E Calvo; Vamsi K Mootha; Michael T Ryan; Yasushi Okazaki; David A Stroud; Cas Simons; John Christodoulou; David R Thorburn Journal: Med (N Y) Date: 2020-07-09
Authors: Lisa T Emrick; Jill A Rosenfeld; Seema R Lalani; Mahim Jain; Nilesh K Desai; Austin Larson; Kimberly Kripps; Adeline Vanderver; Ryan J Taft; Krista Bluske; Denise Perry; Honey Nagakura; LaDonna L Immken; Lindsay C Burrage; Carlos A Bacino; John W Belmont; Undiagnosed Diseases Network; Brendan Lee Journal: Genet Med Date: 2018-12-20 Impact factor: 8.822