Reducing the search space for causal genetic variants with VASP
Field, Matthew A., Cho, Vicky, Cook, Matthew C., Enders, Anselm, Vinuesa, Carola G., Whittle, Belinda, Andrews, T. Daniel, and Goodnow, Chris C. (2015) Reducing the search space for causal genetic variants with VASP. Bioinformatics, 31 (14). pp. 2377-2379.
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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.
| Item ID: | 43593 |
|---|---|
| Item Type: | Article (Research - C1) |
| ISSN: | 1367-4811 |
| Additional Information: | © The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. Source code available for academic non-commercial research purposes at https://github.com/mattmattmattmatt/VASP |
| Date Deposited: | 14 Apr 2016 00:17 |
| FoR Codes: | 06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics @ 25% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 25% 08 INFORMATION AND COMPUTING SCIENCES > 0803 Computer Software > 080301 Bioinformatics Software @ 50% |
| SEO Codes: | 89 INFORMATION AND COMMUNICATION SERVICES > 8902 Computer Software and Services > 890299 Computer Software and Services not elsewhere classified @ 100% |
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