ANNOVAR is a command-line driven software tool and can be used as a standalone application on diverse hardware systems where standard Perl modules are installed. ANNOVAR is open-source, and is freely available at http://www.openbioinformatics.org/annovar/ to the academic community. ANNOVAR takes text-based input files, where each line corresponds to one genetic variant, including SNVs, insertions, deletions or block substitutions. In each line, the first five space- or tab- delimited columns represent chromosome, start position, end position, the reference nucleotide(s) and the observed nucleotide(s). For chromosome positions, ANNOVAR can handle 1-based coordinate system (by default) and half-open zero-based coordinate system (via the use of ‘–zerostart’ argument). Additional columns can be supplied and will be printed out in identical form in output files. For convenience, users can use ‘0’ to fill in the reference nucleotides, if this information is not readily available. Insertions, deletions or block substitutions can be readily represented by this simple file format, by using ‘–’ to represent a null nucleotide. One example is given in Table 1, with extra columns that serve as comments on the variants. Table 1.Example of an input file with five genetic variantsChromosomeStartEndRefObsComments164930342749303427CTR702W (NOD2)164932127949321279−Cc.3016_3017insC (NOD2)131966168519661685G−35delG (GJB2)11052937541052937550ATAAABlock substitution11313388013133881TC−2-bp deletion (rs59770105)
