Finding deleterious score from just RSID
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5.5 years ago

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!

rsid annotation deleterious score • 1.3k views
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5.5 years ago

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

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

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You can convert those to vcf using dbSNP batch mode

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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?

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

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