Question: Annotate Ref/Alt for a list of rsIDs?
0
gravatar for blazer9131
21 months ago by
blazer913110
United States
blazer913110 wrote:

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.

snp dbsnp • 1.1k views
ADD COMMENTlink written 21 months ago by blazer913110
1

How large is large? Give us a number.

Also, I assume single species?

ADD REPLYlink modified 21 months ago • written 21 months ago by Emily_Ensembl18k

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

ADD REPLYlink modified 21 months ago • written 21 months ago by blazer913110

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

ADD REPLYlink written 21 months ago by Kevin Blighe44k
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