dbSNP Batch Query service will be discontinued June 2018: alternatives?
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6.6 years ago

I occasionally use and/or recommend dbSNP batch query service to search rs-IDs and get for example the coordinates.

Today I read that the batch query service will be discontinued in June. See also this post. (Has been announced in July apparently but I missed it then).

What are good alternatives, optionally web-based?

dbsnp • 3.0k views
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6.6 years ago
GenoMax 146k

snp-nexus

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6.6 years ago

My suggestion would be to download the dbSNP vcf file of interest and query it using Unix tools, bcftools etc. But I guess that doesn't work...? What about ensembl/biomart with dataset "Human Short Variants"? You can select as filter "Variant source: dbSNP" and put your IDs in "Filter by Variant name". There is also a biomart package for R.

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For me personally, those options would all work, but none of those is as convenient as justing putting your rs IDs in the field and getting the results.

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