sequence-level feature annotations. Additionally, ANNOVAR can evaluate and filter out subsets of variants that are not reported in public databases such as dbSNP and the 1000 Genomes Project. Typically, rare variants causing Mendelian diseases are less likely to be present in these databases, or are unlikely to be present with high allele frequencies. This rationale has been used to enrich for subsets of variants in previous exome sequencing projects that identified causal mutations for Freeman–Sheldon syndrome (11) and Miller syndrome (3). ANNOVAR offers similar functionality but can extend the comparisons to other public databases such as the 1000 Genomes Project, which offers allele frequency information. Similarly, ANNOVAR can also filter variants against a user-compiled data set, such as all SIFT scores for all possible non-synonymous mutations in the human genome.
