Annotating VCF files

kasthuri · 06-28-2011, 04:00 PM

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:PH5UH7Pa@ftp.broadinstitute.org

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 · 06-29-2011, 03:55 AM

Maybe, try this one:
ftp://gatk-ftp:PH5UH7Pa@ftp.broadinstitute.org/refGene/

ulz_peter · 06-29-2011, 03:59 AM

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

kasthuri · 06-29-2011, 08:10 AM

Quote:

Originally Posted by genomicist

Maybe, try this one:
ftp://gatk-ftp:PH5UH7Pa@ftp.broadinstitute.org/refGene/

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

kasthuri · 06-29-2011, 08:11 AM

Quote:

Originally Posted by ulz_peter

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

Thanks ulz_peter, I am looking into this now.

kasthuri · 06-29-2011, 09:10 AM

Quote:

Originally Posted by ulz_peter

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

Thank you for this wonderful suggestion. ANNOVAR is great!

krawitz · 07-16-2012, 02:44 AM

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 · 07-16-2012, 08:50 PM

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.

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06-28-2011, 04:00 PM	#1
kasthuri Member Location: United States Join Date: Jun 2011 Posts: 36	Annotating VCF files 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:PH5UH7Pa@ftp.broadinstitute.org 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.

06-29-2011, 03:55 AM	#2
genomicist Member Location: Sweden Join Date: Jan 2011 Posts: 12	Maybe, try this one: ftp://gatk-ftp:PH5UH7Pa@ftp.broadinstitute.org/refGene/

06-29-2011, 03:59 AM	#3
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	try annovar: http://www.openbioinformatics.org/annovar/

07-16-2012, 02:44 AM	#7
krawitz Member Location: Bonn Join Date: Feb 2010 Posts: 30	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,...

07-16-2012, 08:50 PM	#8
adamyao Member Location: Taiwan Join Date: Feb 2011 Posts: 19	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.