Retrieve chromosome ID using rsid

Question

[Thorerges]

I have ~500,000 rsids - in the following format

MarkerName A1 A2 
rs2326918 a g 
rs7929618 c g 
rs66941928 t c

I want the chromosome number associated with each MarkerName. So the output would be like this:

MarkerName A1 A2 Chr
rs2326918 a g     6 
rs7929618 c g     6
rs66941928 t c    6

I don't care about A1/A2, I just need the chromosome number. How can i do this?

[cpad0112]

join on rsid with dbsnp vcf.

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db snp -query rs2326918 | esummary | xtract -pattern DocumentSummary -element CHR,CHRPOS,SPDI
6       6:130518946     NC_000006.12:130518945:A:G
6       6:130518946     NC_000006.12:130518945:A:G