Annotate Ref/Alt for a list of rsIDs?
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4.1 years ago
blazer9131 ▴ 20

Hi,

I have a large list of rsIDs from dbSNP. I would like to get the ref/alt for each of the snps. What would be the best way of handling this? It's a VCF containing position and dbSNP id, but no ref/alt columns.

Thanks.

dbSNP snp • 2.3k views
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How large is large? Give us a number.

Also, I assume single species?

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It's roughly 600k IDs. And yes, human.

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My first thought would be to download the latest version of dbSNP in VCF format and then use Python, grep, or BCFtools to pull out the information that you need.

dbSNP in VCF can be downloaded from here: https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/

I reckon that it would take a good few hours to pull out all info.

Kevin

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6 months ago
binodregmi30 ▴ 10

bcftools annotate -a dbsnp.vcf -c ID -o output.vcf input.vcf.compressed.indixed.vcf.gz should work

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