Reducing the search space for causal genetic variants with VASP

Journal Publication ResearchOnline@JCU
Field, Matthew A.;Cho, Vicky;Cook, Matthew C.;Enders, Anselm;Vinuesa, Carola G.;Whittle, Belinda;Andrews, T. Daniel;Goodnow, Chris C.
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.

Journal

Bioinformatics

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Volume

31

ISBN/ISSN

1367-4811

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Issue

14

Pages Count

3

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Publisher

Oxford University Press

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EISSN

N/A

DOI

10.1093/bioinformatics/btv135