how to use sumstats from other methods(except bolt-lmm refered in WIKI) in PolyPred?

[Y-Isaac]

HI,

I noticed that in the WIKI about PolyPred, the result generated by the parameter --predBetasFile in bolt-lmm was used as an estimate of the effect size of the tag SNP. But my association analysis was done using GCTA, and so far I haven't found any similar parameter in GCTA. I have reviewed the example files provided in the file "polypred_example" and noticed that the bolt.beta contains much fewer SNPs than the bolt.sumstats.txt. I would like to ask what exactly happened during this process (I couldn't find the answer in the official manual of bolt-lmm)? Did it performs a process similar to "clustering and thresholding" to only include those Lead SNPs? And can I manually process the summary data generated by GCTA to achieve the same effect as bolt-lmm in WIKI?

Thanks in advanced for your help!

best regards, Issac