Question: Tools to identify biologically relevant SNP calls from a vcf file
1
gravatar for Dataminer
5.0 years ago by
Dataminer2.6k
Netherlands
Dataminer2.6k wrote:

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 tools • 1.8k views
ADD COMMENTlink modified 4.8 years ago by mandecent.gupta0 • written 5.0 years ago by Dataminer2.6k

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

ADD REPLYlink written 4.8 years ago by mandecent.gupta0

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

ADD REPLYlink written 14 months ago by RamRS24k
4
gravatar for laihui126cn
5.0 years ago by
laihui126cn40
Australia
laihui126cn40 wrote:

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

Get it here.

ADD COMMENTlink written 5.0 years ago by laihui126cn40
2
gravatar for Denise - Open Targets
5.0 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

SIFT and PolyPhen are in VEP by default but VEP has got additional plugins including dbNFSP. See C: Prediction of the functional effect of nsSNPs  for more details.

ADD COMMENTlink written 5.0 years ago by Denise - Open Targets5.0k
0
gravatar for Zev.Kronenberg
5.0 years ago by
United States
Zev.Kronenberg11k wrote:

If a commercial solution works for you:

http://www.omicia.com/technology/

If you only have a single individual try Phevor:

http://weatherby.genetics.utah.edu/cgi-bin/Phevor/PhevorWeb.html

ADD COMMENTlink modified 4.8 years ago by RamRS24k • written 5.0 years ago by Zev.Kronenberg11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2331 users visited in the last hour