Question: dbSNP Batch Query service will be discontinued June 2018: alternatives?
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gravatar for WouterDeCoster
3 months ago by
Belgium
WouterDeCoster29k wrote:

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 • 156 views
ADD COMMENTlink modified 3 months ago by dariober9.2k • written 3 months ago by WouterDeCoster29k
1
gravatar for genomax
3 months ago by
genomax49k
United States
genomax49k wrote:

snp-nexus

ADD COMMENTlink written 3 months ago by genomax49k
2
gravatar for dariober
3 months ago by
dariober9.2k
Glasgow - UK
dariober9.2k wrote:

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by dariober9.2k

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.

ADD REPLYlink written 3 months ago by WouterDeCoster29k
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