This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Tools to identify biologically relevant SNP calls from a vcf file

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

snp
• 4,011 views • link
updated by Ram Ram • written by Dataminer Dataminer

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

• 0 views • link
written by mandecent.gupta • mandecent.gupta

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

• 1 views • link
written by Ram Ram

3 answers

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

Get it here.

• 0 views • link
updated by Ram Ram • written by laihui126cn • laihui126cn

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

• 0 views • link
updated by Ram Ram • written by Denise CS Denise CS

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

If you only have a single individual try Phevor.

• 0 views • link
updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

Log in to answer this question.

More posts like this