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How to convert ss to rsid (SNPs)

Hi everybody! I have a long list of submitted SNPs (ss) and I would like to convert them to rsid nomenclature. I know I can do this one by one using dbSNP but how can I do this in batch mode? Thanks!!

snps
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updated by GenoMax GenoMax • written by mendonca_thiago22 • mendonca_thiago22

Have you tried eutills/edirect?

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written by Ram Ram

Can you provide a couple of examples?

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written by GenoMax GenoMax

I have a list like this comprising 43.000 ss:

ss68767636
ss68769665
ss68769692
ss68769749
ss68771111
ss68772343
ss68774024
ss68776006
ss68779227

If I search ss68767636 on dbSNP I get -> rs1381888

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written by mendonca_thiago22 • mendonca_thiago22

If you use the method method below be sure to sign up for and use NCBI_API_KEY. Add in a sleep 2 directive since you are processing thousands of queries.

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written by GenoMax GenoMax

Please accept GenoMax's answer below.

Upvote|Bookmark|Accept

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written by Ram Ram

1 answer

Using EntrezDirect:

$ more id
ss68767636
ss68769665
ss68769692
ss68769749
ss68771111
ss68772343
ss68774024
ss68776006
ss68779227

$ for i in `cat id`; do printf ${i}"\n"; esearch -db snp -query ${i} | esummary | xtract -pattern DocumentSummary -element SNP_ID; printf "\n";done
ss68767636
1381888
1381888

ss68769665
1796935
1796935
1796935

ss68769692

ss68769749
227104
227104
227104

ss68771111

ss68772343
6683621
6683621
6683621
6683621

ss68774024
4658257
4658257
4658257
4658257

ss68776006

ss68779227
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written by GenoMax GenoMax

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