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Old 06-28-2011, 05:00 PM   #1
kasthuri
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Default 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.
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Old 06-29-2011, 04:55 AM   #2
genomicist
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Maybe, try this one:
ftp://gatk-ftp:PH5UH7Pa@ftp.broadinstitute.org/refGene/
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Old 06-29-2011, 04:59 AM   #3
ulz_peter
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try annovar:
http://www.openbioinformatics.org/annovar/
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Old 06-29-2011, 09:10 AM   #4
kasthuri
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Quote:
Originally Posted by genomicist View Post
The problem is the shortcut in their folders are not working on the above mentioned ftp site.
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Old 06-29-2011, 09:11 AM   #5
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Quote:
Originally Posted by ulz_peter View Post
Thanks ulz_peter, I am looking into this now.
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Old 06-29-2011, 10:10 AM   #6
kasthuri
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Quote:
Originally Posted by ulz_peter View Post
Thank you for this wonderful suggestion. ANNOVAR is great!
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Old 07-16-2012, 03:44 AM   #7
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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,...
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Old 07-16-2012, 09:50 PM   #8
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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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