Using HAPSEG and ABSOLUTE in GenePattern


There are 4 modules and one manual step in the usual workflow of using HAPSEG and ABSOLUTE in GenePattern. 

  1. HAPSEG takes single nucleotide polymorphism (SNP) microarray data and outputs copy number data segmented by haplotype.
  2. These data are used by ABSOLUTE to determine possible models for absolute copy numbers per cancer cell from a mixed DNA population. 
  3. 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. 
  4. 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.
  5. The annotated file and the modes file are taken by the module, which outputs the data for the selected ABSOLUTE solution.