Annotate A Vcf File

Question

[win]

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.

[Zev.Kronenberg]

Try VAT in the VAAST pipeline.

[k.kathirvel93]

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

Answer 1

[Pierre Lindenbaum]

• ENSEMBL VEP: http://www.ensembl.org/Homo_sapiens/UserData/UploadVariations
• UCSC : http://genome.ucsc.edu/cgi-bin/hgVai
• SeattleSeq Annotation : http://snp.gs.washington.edu/SeattleSeqAnnotation137/
• Variant analysis tool : http://variant.bioinfo.cipf.es/
• VAT: http://vat.gersteinlab.org/
• ...

Update:

• http://funseq.gersteinlab.org/

[win]

thanks, thats awesome.

[Sondes Kalboussi]

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?

[Zev.Kronenberg]

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

[Pierre Lindenbaum]

VEP uses an ontology

Answer 2

[Neilfws]

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.

[Medhat]

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

Answer 3

[galina.erikson]

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