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Reducing the search space for causal genetic variants with VASP


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

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.;
Responsible Garvan Author Prof Christopher Goodnow
Publisher Name Bioinformatics
Published Date 2015-01-01
Published Volume 31
Published Issue 14
Published Pages 2377-9
Status Published in-print
URL link to publisher's version
OpenAccess link to author's accepted manuscript version