Question: output features calculation from various SNP predictor programs
gravatar for arronslacey
6.3 years ago by
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:


curl \
  -F _ggi_project=PPHWeb2 \
  -F _ggi_origin=query \
  -F _ggi_target_pipeline=1 \
  -F UCSCDB=hg19 \
  -F \
  -F _ggi_batch_file=@snp.txt \
  -D -


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?





grantham snp sift polyphen • 1.4k views
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by arronslacey280
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