This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Get the CHR number and POS using rs id

I have a list of rs IDs (>1000) and I would like to know how I can get the chromosome number and the position? TIA

snp id rs chromosome

try dbSNP vcf.

Using Entrezdirect: This will provide location for latest genome release

$ efetch -db snp -id rs555895 | awk -F "<CHRPOS>" '{print $2}' | sed -e 's/\<\/CHRPOS.*//'
10:87961150
$ efetch -db snp -id rs1044322 | awk -F "<CHRPOS>" '{print $2}' | sed -e 's/\<\/CHRPOS.*//'
10:87863566

Thank you ~ can you please suggest, how can I do this for > 1000 SNPs in my list?

0 answers

No answers yet.

Log in to answer this question.