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Motivation: Increasingly, cost effective high-throughput DNA sequencing technologies are being utilized to sequence human pedigrees in order 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 inher-itance patterns. Designed to aggregate data across a sequenced pedigree, VASP allows both powerful filtering and custom prioritiza-tion of both 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 fo