To perform gene-level association analyses, variant annotation information is needed. Our tool provides a streamlined annotation pipeline (see 2.2.1 for details) and can also accept manually curated annotations by users or by other annotation software programs [e.g. snpEff (Cingolani et al., 2012), ANNOVAR (Wang et al., 2010)]. This annotation information can be used to determine the analysis units. In RVTESTS, variant groups may be specified for gene-level association tests. Users can also specify the optimal analysis unit inferred by external programs.
