Tools to identify biologically relevant SNP calls from a vcf file

Question

[Dataminer]

Hi,

I was just curious to know how many tools are available that can help in annotating the vcf files or say any format that can be extracted from the vcf files.

The ones that I know, include:

• SNPEff
• SIFT
• PolyPhen
• CanPredict
• CHASM
• CRAVAT
• PROVEAN

I am more interested in knowing tools that are similar to CHASM & CRAVAT (Cancer related SNPs). But, that does not mean you cannot suggest others.

Please indicate your favorite tool for extracting most/potentially biologically relevant SNPs.

Thank you

[mandecent.gupta]

How can we use annovar to annotate synonymous or non synonymous snps?

[Ram]

Do not add answers unless you're answering the top level question.

Answer 1

[laihui126cn]

I used Ensembl VEP tools , it made a good job helping to annotate my SNPs.

Get it here.

Answer 2

[Denise CS]

SIFT and PolyPhen are in VEP by default but VEP has got additional plugins including dbNFSP. See this for more details.

Answer 3

[Zev.Kronenberg]

If a commercial solution works for you: http://www.omicia.com/technology/

If you only have a single individual try Phevor.