Is there a recommended cutoff for the --minMAC parameter for step2 single variant test. The documentation examples use --minMAC=20 but the default is 0.5. We have compared the results to GENESIS and there does appear to be some inflation on the low minMAC <=10 with the SAIGE results.
Is there a recommended cutoff for the --minMAC parameter for step2 single variant test. The documentation examples use --minMAC=20 but the default is 0.5. We have compared the results to GENESIS and there does appear to be some inflation on the low minMAC <=10 with the SAIGE results.