Is there a way to batch search dbSNP and get ClinVar "clinical significance" (for example, pathogenic or benign) information out?
Instead of doing this manually. Note, I am not looking for tips on how to get SIFT predictions etc - only the information listed in "clinical significance".
Hi Nadia
Have a look at Ensemble website. There is a link for disease and phenotypes. It may helps.
I have no problem finding the information - but I wanted to figure out if the is a way to use it to annotate SNP files or exome files - or simply "batch annotating" a list of risids with clinical significance info. :)
Probably the easiest way is to download the clinvar set as a vcf from the ftp site: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/clinical_vcf_set. The VCF has an info component CLINSIG that has that information
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