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 ==== USAGE ====
 
-./opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE]
+./opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE] [options]
 
  
 ==== DESCRIPTION ====
 
 **We're still in the process of optimising code execution, and recommend chunking the input data into separate files for each chromosome (each one in the format above), and calling each chunk separately in parallel on a different processing node to significantly reduce execution time. **
  
-==== OPTIONS ====
+==== INPUT/OUPUT ====
 
 -in FILE
  
 
 -out FILE
  
-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: rs, coordinate, allelesAB, pertubation value, 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: rs, coordinate, allelesAB, pertubation value, call_1, call_2, call_3,.... The order of the calls/probs is given by the order of the sample ids in the header line of the output 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 more compatible with those of the Illuminus caller, and not reflective of any pertubation analysis. The probs file gives probabilities in the order: P(AA), P(BB), P(AB), P(NN). In cases where the maximum genotype probability is less than the probability threshold, the call will be NN but the posterior probabilities might not have P(NN) as the highest value.
+
+==== OUTLIER HANDLING OPTIONS ====
+
+-nointcutoff
+
+This will stop optiCall excluding outliers with intensity values that are too high. Run this if you already have filtered samples/SNPs for intensity outliers
+
+-meanintfilter
+
+By running this flag, optiCall identifies samples with mean intensity (across SNPs) values that are too high or too low, and excludes them from the clustering. This samples have their genotypes set to NN at all SNPs. If you already deal with outlying intensities before using optiCall, there's no need to use this flag.
+
+-noblank
+
+By default, optiCall calls all samples at a SNPs as NN if the result of genotype clustering produces a Hardy-Weinberg Equilibrium (HWE) p-value of less than optiCall's tbreshold (by default 1e-15). Setting this flag means optiCall will make a call, even if significantly deviated from HWE.
+
+==== THRESHOLD SETTING OPTIONS ====
+
+-hwep NEW_VALUE
+
+By default this is 1e-15. 
+
+-minp NEW_VALUE
+
+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.
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