Entering edit mode
7.4 years ago
punk_e_smurf
•
0
I have a list of just RSIDs, about a million. I wanted to find their deleterious score, like a ClinVar score but I'm not sure what to search against. I know dbSNP has a bunch of dbs and so does ANNOVAR but which one and which DB do I need to search against? I also just need the DBs not a tool because I was planning on putting this as a step in my pipeline and wanted to keep it really simple. Thanks in advance for your help!
So there's a way to get a VCF from just a list of RSIDs?
You can convert those to vcf using dbSNP batch mode
That's one of the problems I have, it's about a million RSIDs and the batch only allows 30k, plus I was hoping to do it programmatically because I needed to put this in my pipeline. Can I just query dbSNP directly?
You could download the dbSNP vcf entirely and
grep -f
the records you need.