158    ◾    Bioinformatics

-build hg19 \

../input/humanSNP.avinput \

humandb/

The above command generates three files with the “humanSNPannot” prefix as shown in

Figure 4.19. The “humanSNPannot.variant_function” file contains annotation for all vari-

ants, by adding two columns to the beginning of each input line (Figure 4.20).

The first column is annotated with the affected part of the gene. The parts can be exonic,

splicing, nrRNA, UTR5, UTR3, intronic, upstream, downstream, or intergenic region. The

second added column annotates the gene name or names.

The second annotation output file, “humanSNPannot.exonic_variant_function”, con-

tains the amino acid changes as a result of the exonic variant (Figure 4.21).

FIGURE 4.19  Variant annotation files.

FIGURE 4.21  Exonic variant function file.

FIGURE 4.20  The ANNOVAR variant annotation file.