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Summary data file

The summary data from a GWAS/meta-analysis should be prepared in COJO format, see below:

SNP A1 A2 FREQ BETA SE P NMISS
M1 G T 0.5181 -1.565 1.155 0.1762 500
M2 A G 0.145 -1.77 1.519 0.2445 500
M3 G A 0.3206 1.498 1.583 0.3445 500
M4 C G 0.5356 0.3366 1.003 0.7374 500
M5 C G 0.0975 1.27 1.755 0.4695 500

Columns are SNP, the effect allele, the other allele, frequency of the effect allele, effect size, standard error, p-value and sample size. Note that “A1” needs to be the effect allele with “A2” being the other allele, and “FREQ” should be the frequency of “A1”.

The file should be assigned to parametric option --sumstat.