Get the CHR number and POS using rs id
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3.1 years ago
Mahan ▴ 70

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 • 1.5k views
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try dbSNP vcf.

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

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