Question: output features calculation from various SNP predictor programs
0
gravatar for arronslacey
6.3 years ago by
arronslacey280
United Kingdom
arronslacey280 wrote:

Hi - I want to collect information on SNPs that are often used to predict how damaging they are. 

For example - using polyphen I can output not only the score, but all the features (MSA, domain regions etc) that were used to calculate the score by using the SNPFUNC parameter:

 

#!/bin/sh
curl \
  -F _ggi_project=PPHWeb2 \
  -F _ggi_origin=query \
  -F _ggi_target_pipeline=1 \
  -F MODELNAME=HumDiv \
  -F UCSCDB=hg19 \
  -F SNPFUNC= \
  -F NOTIFYME=me@gmail.com \
  -F _ggi_batch_file=@snp.txt \
  -D - http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi

 

which I find very useful as I can use these features to feed into a machine learning process. I am currently trying to do this with SIFT but cannot determine if this is possible. I have used VEP which can produce some SNP annotation, but VEP just querey's against a database that contains such information, rather than calculate it's own score.

 

is anyone aware of other prediction tools that output their features as well as score?

 

thanks.

 

arron

grantham snp sift polyphen • 1.4k views
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by arronslacey280
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: 2098 users visited in the last hour
_