How to download database for annotating snps?
Hi,
I have snp list and I need to annotate them with the following features.
- Downstream
- Non Sysnonymous
- Synonymous
- UTR3
- UTR5
- Upstream
- Intron
Can you pls suggest me tool or database for annotating snps with above features.
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mandecent.gupta •
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mandecent.gupta •
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Hello mandecent.gupta!
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Annovar is good tool but there is no info about annotating snps with synonymous or non synonymous. Also I could not find info on the link as well.
Search biostars for SNpEFF or VariantEffectPredictor
When I run ANNOVAR it creates a file with the file extension
.exonic_variant_function. it lists all variants in exons, and the first column reads "nonsynonymous" or "synonymous".Did you try using the tool at all? Do look at the output files.