Reducing the search space for causal genetic variants with VASP

Bioinformatics. 2015 Jul 15;31(14):2377-9. doi: 10.1093/bioinformatics/btv135. Epub 2015 Mar 8.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Female
  • Genetic Linkage*
  • Genetic Markers / genetics
  • Genetic Predisposition to Disease*
  • Genetic Variation / genetics*
  • Heterozygote
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • INDEL Mutation / genetics
  • Male
  • Pedigree
  • Polymorphism, Single Nucleotide / genetics
  • Software*


  • Genetic Markers