Multiple annotations using annovar?

Question

[arronslacey]

Hi - is it possible to add multiple annotations in the same command with annovar. For example annotation with both exac and 1000g? The command for one is this:

perl annotate_variation.pl -filter -build hg19 -dbtype exac03  GLRA1.txt humandb/

so I have tried

perl annotate_variation.pl -filter -build hg19 -dbtype exac03 -dbtype 1000g2015aug_eur GLRA1.txt humandb/

and

perl annotate_variation.pl -filter -build hg19 -dbtype exac03,1000g2015aug_eur GLRA1.txt humandb/

but both do not work. I just wondered if annovar has this functionality or if I will have to write a script.

cheers!

Answer 1

[igor]

There is actually a separate script table_annovar.pl you can use for this. It generates an output file with many columns, each representing one set of annotations.

It's described in more detail here: http://annovar.openbioinformatics.org/en/latest/user-guide/startup/

[arronslacey]

excellent thanks very much!

[arronslacey]

just one thing - table_annovar.pl does not seem to preserve additional custom fields specified in the input file, where annotate_variation.pl appears to do this.

do you happen to know how to keep extra columns in the input? all my additional columns are in the format

comments: field1   field2

[igor]

I use unix join to merge the input and output tables.