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 The batchid is designed to account for possible batch/ethnicity heterogeneity. For example when optiCall calculates hardy-weinberg equilibrium, calling different ethnicities together could pose a problem. To handle this, give a separate batchid to each unique group being called. Batchids are integers greater than or equal to 0, and a batch id of -9 will exclude the sample from any hardy-weinberg equilibrium calculations. 
 
 
+==== X,Y Chromosome, and Mitochondrial DNA calling ====
 
+simply run optiCall as normal but including the flag -X, -Y or -MT corresponding to the type of data you're trying to call.