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 -in FILE
  
-The input intensity file name, in the format specified above
+The input intensity file name, including the path
 
 -out FILE
  
-The output file name. Two files will be created by the algorithm with the filepath specified. One will have the suffix '.calls' appended to it for the genotype calls, and the other '.probs' for the posterior probabilities. The output format is space-delimited with columns: coordinate, rs, pertubation value, allelesAB, call_1, call_2, call_3,.... The order of the calls is the same as the header from the input file. The calls are encoded as 1 = AA, 2 = AB (heterozygote), 3 = BB, 4 = NN (no call). The pertubation value is merely output to make call files compatible with those of the Illuminus caller, and not reflective of any pertubation analysis. 
+The output file name, including the path. Two files will be created by the algorithm with the filepath specified. One will have the suffix '.calls' appended to it for the genotype calls, and the other '.probs' for the posterior probabilities. The output format is space-delimited with columns: coordinate, rs, pertubation value, allelesAB, call_1, call_2, call_3,.... The order of the calls is the same as the header from the input file. The calls are encoded as 1 = AA, 2 = AB (heterozygote), 3 = BB, 4 = NN (no call). The pertubation value is merely output to make call files compatible with those of the Illuminus caller, and not reflective of any pertubation analysis. 
 
 
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