Variant Discovery    ◾    151

Figure 4.15 shows the number of effects by type and region. Figure 4.16 shows a bar

chart showing the percentage of effects by region.

4.3.3  ANNOVAR

ANNOVAR [13] is one of the most commonly used annotation tools that is used to anno-

tate SNVs and InDels with different types of annotations including functional conse-

quence on genes, inferring cytogenetic bands, functional importance, impacts of variants

in conserved regions, and identifying variants reported in the NCBI dbSNP and the 1000

FIGURE 4.14  Variant effect summary.

FIGURE 4.13  SnpEff annotation summary.