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Kyoko-wtnb / gwasatlas

Source code for GWAS atlas web application
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Harmonized GWAS summary statistics #1

Open Shicheng-Guo opened 3 years ago

Shicheng-Guo commented 3 years ago

Dear Kyoko,

I am wondering whether Harmonized GWAS summary statistics is available from GWAS atlas? I want to download some disease specific GWAS statistics from GWAS atlas to follow by MTAG meta-analysis.

Thanks.

Shicheng

bschilder commented 3 years ago

I 2nd this, GWAS Atlas is a great resource but reharmonizing all of the GWAS sum stats from their original sources isn't possible for most labs.

Sharing the harmonized summary stats would be huge boost for reproducibility of the work presented in the associated paper, as well as allowing for extension of these analyses. There were also SNP-level fine-mapping analyses presented in this paper but I can't seem to find them shared anywhere (in the Supp Tables or GWAS Atlas). These would also be super helpful.

@Kyoko-wtnb, any thoughts on this?

Many thanks, Brian

bschilder commented 3 years ago

Just found this @Shicheng-Guo; merged UKB v2 sum stats, which constitutes 600/4,756 of the GWAS in GWAS Atlas. https://ctg.cncr.nl/software/summary_statistics

Shicheng-Guo commented 3 years ago

Thank you Brian!! which is really helpful!!

Guo00158 commented 2 years ago

Hi Shicheng, I also want to harmonize the GWAS summary data from the atlas but I don't find the effect allele frequency in the summary statistics. Only MAF exists in the data and I'm sure whether effect allele or non-effect allele is the minor allele. I wonder if you have figured them out. Thank you! @Shicheng-Guo