Tools to identify biologically relevant SNP calls from a vcf file
3
1
Entering edit mode
9.9 years ago
Dataminer ★ 2.8k

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 • 3.2k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
4
Entering edit mode
9.9 years ago
laihui126cn ▴ 40

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

Get it here.

ADD COMMENT
2
Entering edit mode
9.9 years ago
Denise CS ★ 5.2k

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

ADD COMMENT
0
Entering edit mode
9.9 years ago

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

If you only have a single individual try Phevor.

ADD COMMENT

Login before adding your answer.

Traffic: 1178 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6