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 NOTIFYMEfirstname.lastname@example.org \ -F email@example.com \ -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?