How To Annotate The Snps Produced By Gatk?

Question

[xiaoguang]

Hi guys,

I'm a new bioinformatic researcher, would like to learn something from you.

Now the problem is I got vcf files of SNPs produced by GATK, I want to annotate them. Could some one give me a workflow? I need more detail such like comand line step by step.

All answers are appreciated!

Xg

[Pierre Lindenbaum]

http://www.broadinstitute.org/gatk/guide/tagged?tag=annotation

Answer 1

[Kasthuri]

Annovar (http://www.openbioinformatics.org/annovar/) has a script (perl module) that can convert the vcfs to annovar format which can then be annotated.

For instance using hg19 and RefSeq:

{annovar_dir}/convert2annovar.pl  -format vcf4 {variants}.vcf > variant.annovar.format
{annovar_dir}/annotate_variation.pl -build hg19  --geneanno -dbtype refGene variant.annovar.format {annovar_dir}/humandb/

Of course, this assumes you already have hg19 downloaded to annovar humandb directory. If you don't have it you can download it using '-downdb' option. Refer to their manual for details.

[xiaoguang]

Thank u very much. Actually, I've tried many times by using snpEff which doesn't need to convert the fomat of my vcfs, but there are still some errors when I built the new database(Refseq). I also did it by Galaxy, unfortunately, there is no genome Ref of Vitis. Anaway, II will follow your suggestion and let you know the results :P

[Pablo]

You don't need to create a database yourself. Just install hg19 by running java -jar snpEff.jar download -v hg19