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Reducing the search space for causal genetic variants with VASP

Abstract

MOTIVATION: Increasingly, cost-effective high-throughput DNA sequencing technologies are being utilized to sequence human pedigrees to elucidate the genetic cause of a wide variety of human diseases. While numerous tools exist for variant prioritization within a single genome, the ability to concurrently analyze variants within pedigrees remains a challenge, especially should there be no prior indication of the underlying genetic cause of the disease. Here, we present a tool, variant analysis of sequenced pedigrees (VASP), a flexible data integration environment capable of producing a summary of pedigree variation, providing relevant information such as compound heterozygosity, genome phasing and disease inheritance patterns. Designed to aggregate data across a sequenced pedigree, VASP allows both powerful filtering and custom prioritization of both single nucleotide variants (SNVs) and small indels. Hence, clinical and research users with prior knowledge of a disease are able to dramatically reduce the variant search space based on a wide variety of custom prioritization criteria. AVAILABILITY AND IMPLEMENTATION: Source code available for academic non-commercial research purposes at https://github.com/mattmattmattmatt/VASP.

Type Journal
ISBN 1367-4811 (Electronic) 1367-4803 (Linking)
Authors Field, M. A.; Cho, V.; Cook, M. C.; Enders, A.; Vinuesa, C. G.; Whittle, B.; Andrews, T. D.; Goodnow, C. C.;
Garvan Authors Prof Christopher Goodnow
Publisher Name BIOINFORMATICS
Published Date 2015-01-01 00:00:00
Published Volume 31
Published Issue 14
Published Pages 2377-9
URL http://www.ncbi.nlm.nih.gov/pubmed/25755272
Status Published In-print
OpenAccess Link https://publications.gimr.garvan.org.au/download.php?13159_13296/btv135.pdf