Annotating VCF files

[kasthuri]

Can anybody tell me how to annotate vcf files for hg19 aligned file? I tried GATK, vcftools and vcfCodingSnps.

GATK - I couldn't find their refGene file in their ftp server

ftp://gatk-ftp:[email protected]

vcftools: I am having a hard time running it - it gives me "tabix" error

vcfCodingSnps: I was not able to compile on my mac - OS X 10.6, 64 bit
It will be great if anybody can give me a complied code for this architecture.

Thanks.

[genomicist]

Maybe, try this one:
ftp://gatk-ftp:[email protected]/refGene/

[ulz_peter]

try annovar:

http://www.openbioinformatics.org/annovar/

[kasthuri]

Maybe, try this one:
ftp://gatk-ftp:[email protected]/refGene/

The problem is the shortcut in their folders are not working on the above mentioned ftp site.

[kasthuri]

try annovar:
http://www.openbioinformatics.org/annovar/

Thanks ulz_peter, I am looking into this now.

[kasthuri]

try annovar:
http://www.openbioinformatics.org/annovar/

Thank you for this wonderful suggestion. ANNOVAR is great!

[krawitz]

You might also want to try www.gene-talk.de . It is an wiki-like expert platform for filtering and annotating sequence variants. The automatic annotation is based on annovar. For the interpreation of unkown variants other expert users might assist you,...

[adamyao]

Alternatively, direct upload your vcf to MegaQuery of VarioWatch (http://genepipe.ncgm.sinica.edu.tw/v...n.do?mega=true) should receive your results online in real time.