Files changed (1)
- Ignore whitespace
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.
The info file specifies sample genders and also whether samples should be excluded from calling. It is whitespace separated and the format is:
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
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.