I work with nonhuman data. I have a bunch of SNPs that I want to predict how deleterious the SNP is. I know there is software out there like sift, polyphen, and provean. The issue I have is that you have to manually input them. I was wondering if anyone has developed a pipeline to mass submit SNP?
I know you can download polyphen and provean but you have to make a .fasta file and file with the SNPs of interest for every protein. I just don't want to do that for thousands of SNPs
I know Sift is a bit better. You can just run an entire VCF and it will give you predictions for everything at one. However, I think Sift isn't the most accurate.
Does anyone use any other software? or does anyone do something different to predict the effect of SNP a protein?