Finding deleterious score from just RSID

Question

[punk_e_smurf]

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!

Answer 1

[WouterDeCoster]

I would suggest converting those to vcf format and using CADD score for this.

[punk_e_smurf]

So there's a way to get a VCF from just a list of RSIDs?

[WouterDeCoster]

You can convert those to vcf using dbSNP batch mode

[punk_e_smurf]

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?

[WouterDeCoster]

You could download the dbSNP vcf entirely and grep -f the records you need.