I have noticed a similar question has been asked but it was 2.5 years ago -- I wanted to re query to see if a new software package was available.
My goal is to determine if SNPS are in specific annotated domains (eg phosphorylation sites, transmembrane domains, DNA binding domains, etc). I have a vcf files and an annovar annotated worksheet. Does anyone know of an efficient way to accomplish this?
I assume you already have SNP positions located to CDS/cDNA coordinates? If so, I think the best way would be run Pfam in batch and identify the protein domain coordinates and run a simple intersect of the coordinates. I think there are perl modules parsing Pfam results, which could be used to automate this process.
Input your VCF file and add --domains to your command line and you'll get the protein domains. You'll also get any AA changes and you can choose to get SIFT and PolyPhen scores too.
It doesn't do that at the moment, but we're keen to get feedback. If you have a suggestion I can pass that on. I'm not entirely sure what you mean, can you explain further what you'd like to put in and get out?
Did you try SNP tools available on internet and if not then you can visit through snp-nexus, bioinformatics, iconcologia or many other websites for the solution of your query. Even if these tools are unable to meet your desired goal then instead of wasting time, contact any reliable domain provider or experienced web host, as they are experts and would definitely provide you a solution.
I was using Ensembl VEP but didn't know about this! Thanks, Emily!