Family-based sequencing studies enable researchers to identify highly penetrant genetic variants too rare to be tested in conventional case-control studies, by studying co-segregation of variant and disease phenotypes. When multiple affected subjects in a family are sequenced, the probability that a variant or a set of variants is shared identical-by-descent by some or all affected relatives provides evidence against the null hypothesis of complete absence of linkage and association. The Rare Variant Sharing software package RVS implements a suite of tools to assess association and linkage between rare genetic variants and a dichotomous disease indicator in family pedigrees.