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 -hwep NEW_VALUE
-By default this is 1e-15. 
+By default this is 1e-15. This is the threshold Hardy-Weinberg Equilibrium (HWE)  p-value at which optiCall determines a clustering has failed. If the HWE p-value is less than this threshold optiCall will first attempt a rescue clustering for the SNP, and if that fails, call all genotypes at that SNP NN (use the -noblank option to stop this). To get the best calls, we recommend you set this value to the HWE p-value QC threshold for your study
 -minp NEW_VALUE
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