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 https://github.com/mattmattmattmatt/VASP.
|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|
|URL link to publisher's version||http://www.ncbi.nlm.nih.gov/pubmed/25755272|
|OpenAccess link to author's accepted manuscript version||https://publications.gimr.garvan.org.au/open-access/13159|