Predicting Biologically Significant Snps

Question

[Pappu]

I am trying to figure out which SNP might change the structure and function of the translated protein based on the minor allele freq (MAF) >0.1 from 1000 genomes data and ensembl SIFT and Polychen scores. I am wondering if there are any other way of achieving the goal.

Answer 1

[Erik Garrison]

Check out the variant effect predictor. You can use it to get annotations from a number of functional effect prediction systems, such as Gerp and Consed.

Answer 2

[Zev.Kronenberg]

The VAAST pipeline has a variant annotation tool (VAT). In addition the output can be used the GWAS tool VAAST.