+opticall includes all the libraries it needs, and requires nothing beyond the C++ standard. It compiles using g++ on unix/mac based systems.
+You can download the latest release of opticall from:
+download the most recent compressed file in the format you're most comfortable with. In the case of a .gz download, uncompress the file by running:
+which creates a folder of the same name as filename. cd into the optical folder:
+then compile the opticall code by running the make command:
+after which the opticall executable will appear, and you've installed opticall
opticall [options] [-in INPUT_FILE] [-out OUTPUT_FILE]
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 tab separated, with SNPs are rows, and samples as columns. So a line would be:
An example input intensity file is provided with the program for your information.