Annotate A Vcf File
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.
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k.kathirvel93
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win
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win
3 answers
- 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:
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Pierre Lindenbaum
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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Sondes Kalboussi •
Pierre Lindenbaum which do you like best? Which uses a controlled vocabulary?
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Zev.Kronenberg
VEP uses an ontology
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Pierre Lindenbaum
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.
Pierre's list is great. Also try SG-ADVISER: http://genomics.scripps.edu/ADVISER/
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galina.erikson
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