There are 4 modules and one manual step in the usual workflow of using HAPSEG and ABSOLUTE in GenePattern.
- HAPSEG takes single nucleotide polymorphism (SNP) microarray data and outputs copy number data segmented by haplotype.
- These data are used by ABSOLUTE to determine possible models for absolute copy numbers per cancer cell from a mixed DNA population.
- The ABSOLUTE.summarize module takes a file containing a list of ABSOLUTE output files and summarizes them in a format that facilitates the manual review of those results.
- An analyst then manually reviews the data and determines whether to override the best-fit model suggested by ABSOLUTE. Any overrides are noted in an annotated version of the ABSOLUTE calls file.
- The annotated file and the modes file are taken by the ABSOLUTE.review module, which outputs the data for the selected ABSOLUTE solution.