We next examined region-based annotations on the list of variants in Table 1. The ‘–regionanno’ argument needs to be used, and a ‘–dbtype’ argument needs to be specified to select an annotation database. For example, when ‘–dbtype mce44way’ is issued, ANNOVAR will search through the phastConsElements44way annotation. This annotation database contains multiple alignments of 44 vertebrate species and measurements of evolutionary conservation using two methods, phastCons (18) and phyloP (19) on the human genome (UCSC build version: hg18). The second variant (c.3016_3017insC in NOD2) is located in a conserved region, with normalized conservation score of 392. We next used ‘–dbtype segdup’ to identify variants located in segmental duplication regions (20), by examining the genomicSuperDups annotation database. The last variant in Table 1 (rs59770105, a small deletion) is identified within a segmental duplication, with sequence identity of 0.996 with the other copy of the sequence. In addition to the two examples above on region-based annotations, many other annotation databases from UCSC Genome Browser can be also interrogated. Additionally, ANNOVAR implemented the ability to directly interrogate any annotation databases conforming to Generic
