Question: How to change snp ID to Variation ID of Clinvar Database
0
gravatar for cnhuangxy
3.6 years ago by
cnhuangxy0
cnhuangxy0 wrote:

A list of snp ID

e.g.:rs7754840

……

Need  Condition(s)
(Mode of inheritance)

I  searched ClinVar data : XML, TXT, and VCF. No file contain both "snp ID" and "Phenotype" item.

Maybe  I need to chang snp ID to its Variation ID (e.g. Variation ID:986) at first. Then, crawling both item use python.

Dose anyone  had successfully change snp ID to Variation ID of Clinvar database or has more directly solutions.

Thanks for help in advance!

 

 

 

 

snp clinvar python • 2.0k views
ADD COMMENTlink modified 2.4 years ago by m66110220 • written 3.6 years ago by cnhuangxy0
2
gravatar for Newgene
3.1 years ago by
Newgene350
United States
Newgene350 wrote:

Try MyVariant.info API:

http://myvariant.info/v1/query?q=dbsnp.rsid:rs727503873&fields=clinvar

There is a "variant_id" field under "clinvar". Or maybe you don't need variant_id anymore, since you can get back ClinVar annotations from a rsid directly now.

Check out this "Access ClinVar Data from MyVariant.info Services" tutorial. Also this biostar answer:

A: Searching for ClinVar entries based on SNP annotation

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Newgene350
1
gravatar for trausch
3.6 years ago by
trausch1.4k
Germany
trausch1.4k wrote:

With the UCSC Table Browser:

https://genome.ucsc.edu/cgi-bin/hgTables

Select your desired assembly version, group: Phenotype and Literature, track: ClinVar Variants. This table includes the snpID (without the leading rs).

ADD COMMENTlink written 3.6 years ago by trausch1.4k
0
gravatar for m6611022
2.4 years ago by
m66110220
m66110220 wrote:

When I tried this solution, myvariant.info was a bit outdated, but there is another way

In the clinvar FTP site, in the tab deliminated section, there is a file called "Cross References.txt". This will get you from dbsnp ID to allele ID. There is another file called "Variation allele.txt" that can get you from Allele ID to variation ID.

You can read these text files directly from in R or Python. And it will be up to date

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by m66110220
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