Question: dbSNP Batch Query service will be discontinued June 2018: alternatives?
0
gravatar for WouterDeCoster
21 months ago by
Belgium
WouterDeCoster42k 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 • 851 views
ADD COMMENTlink modified 21 months ago by dariober10k • written 21 months ago by WouterDeCoster42k
1
gravatar for genomax
21 months ago by
genomax75k
United States
genomax75k wrote:

snp-nexus

ADD COMMENTlink written 21 months ago by genomax75k
2
gravatar for dariober
21 months ago by
dariober10k
WCIP | Glasgow | UK
dariober10k 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 21 months ago • written 21 months ago by dariober10k

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 21 months ago by WouterDeCoster42k
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