Question: dbSNP Batch Query service will be discontinued June 2018: alternatives?
0
gravatar for WouterDeCoster
12 months ago by
Belgium
WouterDeCoster37k 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 • 511 views
ADD COMMENTlink modified 12 months ago by dariober9.9k • written 12 months ago by WouterDeCoster37k
1
gravatar for genomax
12 months ago by
genomax64k
United States
genomax64k wrote:

snp-nexus

ADD COMMENTlink written 12 months ago by genomax64k
2
gravatar for dariober
12 months ago by
dariober9.9k
WCIP | Glasgow | UK
dariober9.9k 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 12 months ago • written 12 months ago by dariober9.9k

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 12 months ago by WouterDeCoster37k
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