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-
 
 USAGE
-            opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE]
+
+opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE]
  
  
 DESCRIPTION
+
+opticall reads in file of intensity data (currently Illumina normalized intensities) and clusters them considering both per-SNP and per-sample information, and provides genotype calls as output. The input file is in the format (columns: rs, coord, allelesAB, id_1a, id_1b, id_2a, id_2b, etc)
  
-The code reads in a text file (columns: rs, coord, allelesAB, id_1a, id_1b, id_2a, id_2b, etc), and iterates using an EM algorithm to a convergent set of calls. 
  
+OPTIONS
+
+-in FILE
+ 
+The input intensity file name, in the format specified above
+
+-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, perturbation score, 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).
+
+-inblock FILE
+
+The input intensity file name, in the format specified above
 
  
- 
-OPTIONS
- 
-            -in FILE
- 
-The input file name, in the format 
- 
-            -out FILE
- 
-The output file name. This will have the suffix '.calls' appended to it for the genotype calls and '.probs' for the posterior probabilities. The output format is space-delimited with columns: coordinate, rs, perturbation score, 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).
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