By default this is 0.7. This is the threshold at which optiCall will make a call. If no posterior genotype probability is above this value, then optiCall sets the genotype to NN.
-==== PROVIDING SAMPLE INFORMATION & CALLING SUBSETS ====
+==== PROVIDING SAMPLE INFORMATION & CALLING SUBSETS ====
The info file specifies sample genders and also whether samples should be excluded from calling. It is whitespace separated and the format is:
-sampleid gender excludeflag
+sampleid gender excludeflag
with a line for all the samples in the intensity data supplied. An example info file is provided with the optiCall download.
-sampleid should match the sampleid given in the header of the intensity file.
-gender is either 1 for male or 2 for female - and any other integer value is considered as unknown
+sampleid should match the sampleid given in the header of the intensity file. gender is either 1 for male or 2 for female - and any other integer value is considered as unknown
excludeflag is 1 if the sample is to be excluded from calling, or zero if it is to be included in calling.
+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.