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/)

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