notes of ANNOVAR

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->-。

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