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  2. optiCall

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 USAGE
 
 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)
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+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 intensity input file is space separated, with SNPs are rows, and samples as columns. 
+
+So a line would be: rsid rscoord allelesAB id_1a id_1b id_2a id_2b etc.
+
+where id_1a is the allele A intensity value for sample 1, and id_1b is the allele B intensity value for sample 1. The algorithm is known to perform well with Illumina normalized intensities.
+
  
 OPTIONS
 
 
 -inblock FILE
 
-The input intensity file name, in the format specified above
+Another input intensity file name, in the format specified above, used to define regions for genotypes, in case you need regions defined from a different dataset.