GWAS without allelle frequency data

zhilizheng / SBayesRC

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GWAS without allelle frequency data #40

Open diegoortunes opened 1 month ago

diegoortunes commented 1 month ago

Hi, Zhili. I am currently running SBayeRC for the first time on a phenotype of Anorexia Nervosa. The GWAS dataset I am utilizing is from 2019, which I have used in other approaches. However, I have encountered an issue as the dataset does not include information on the allele frequency of the effect variant, an information that SBayesRC used as input. I would like to know how to deal with this situation, is it possible to obtain the beta effect without the allele frequency data?

zhilizheng commented 4 weeks ago

Hi @diegoortunes ,

The allele frequency is only used for the QC purpose. If you are sure about the quality, you can fill the allele frequency with our LD information (LD_folder/snp.info).

Regards, Zhili