1. 坐标系: By default, 1-based coordinate system is used.
2. 核心程序: annotate_variation.pl
3. 注释类型: gene-based (-geneanno), region-based (-regionanno) and filter-based (-filter) annotations.
4. 输出结果:
a. The first file contains annotation for all variants, by adding two columns to the beginning of each input line.
b. The second output file contains the amino acid changes as a result of the exonic variant.
5. 重点定位：
What about GFF3 file for new species?（http://annovar.openbioinformatics.org/en/latest/user-guide/gene/）
gff3ToGenePred （http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/）
6.特别注意：
annovar注释以后，会把InDel的坐标改了。比如：
原来是， 133，ACTG->A，
修改后是，134，CTG->-。