Annotate A Vcf File
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11.2 years ago
win ▴ 990

hi all, i was wondering if someone could help. i wanted to know which annotation programs for VCF file especially the online ones. any place there might be a list?

thanks in advance.

vcf annotation • 18k views
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Try VAT in the VAAST pipeline.

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Can Anyone help ? I want to annotate my bacterial genomes vcf file (P.aeruginosa) . Suggestions pls ..

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thanks, thats awesome.

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Did you use Annovar for bacterial genome annotation before and what is the best one among the previous list for bacteria based on your experience?

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Pierre Lindenbaum which do you like best? Which uses a controlled vocabulary?

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VEP uses an ontology

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11.2 years ago
Neilfws 49k

I'd add snpEFF to the list. Also, recommended by others but I have not tried it - exome variant server; see "how to use" tab for a client download.

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very good tool specially if you are not working with human or model organism as you can make your own db

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11.2 years ago

Pierre's list is great. Also try SG-ADVISER: http://genomics.scripps.edu/ADVISER/

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