Question: How to download SNPs from two SNP databases
0
gravatar for Ashley
2.8 years ago by
Ashley50
China
Ashley50 wrote:

To assess SNPs in different genomic elements, we downloaded two SNP databases: (1) 12,891 SNPs from the National Human Genome Research Institute’s GWAS catalogue (https://www.genome.gov/26525384); (2) 14,416,369 common SNPs from dbSNP Build 142 common (downloaded from the UCSC Genome Browser) (treated as background variation). (PMCID: PMC5316832) I want to known where the 12,891 SNPs come from. My workflow is as follows: Step1: open the database: http://www.ebi.ac.uk/gwas/docs/file-downloads Step2: click on "All associations" and download. Step3: filter SNPs by p-value<1 × 10−5 (PMCID: PMC3965119) Step4: count the uniq SNPs However, the number of uniq SNPs is not 12,891. I want to known why and how? Thank you very much!

snp • 1.6k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Ashley50
1

Hi ,

What do you mean by uniq SNPs can you give us example ?

Best

ADD REPLYlink written 2.8 years ago by Titus910
0
gravatar for Ashley
2.8 years ago by
Ashley50
China
Ashley50 wrote:

I have solved this question by sending email from certain authors. Thanks!

ADD COMMENTlink written 2.8 years ago by Ashley50
1

May be you can share your solution it could help someone else in the future :)

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Titus910
0
gravatar for Ashley
2.8 years ago by
Ashley50
China
Ashley50 wrote:

(1)The GWAS SNPs are always updated. It is not surprising that the number is different. (2)The common SNP in dbSNP build 142 common and all SNPs is different.

ADD COMMENTlink written 2.8 years ago by Ashley50
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