I am using PRSice software for Polygenic risk score calculation of complex diseases like Type 2 Diabetes, Coronary artery disease. Input files required for analysis are Base file (example: TOY_BASE_GWAS.assoc ) and target file (binary files from plink for your target data). I am able to create target files using plink plug in from genome studio .,but Don't know how to create gwas association file for my phenotype like Type 2 Diabetes
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Thank you. I have downloaded association results from GWAS. The file has all required columns except effect size estimates, is there is any way to calculate it ? or is PRSice can run without effect size info in base file.
{PRSice requires the base file to contain information of the effective allele (--A1), effect size estimates (--stat)}
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