I am trying to determine the purity and ploidy of my WES samples using ABSOLUTE. I have normal, primary and metastasized samples. Some of the samples failed ABSOLUTE. Here is an example from the error file:
 "Capping 13 segs at tCR = 5.0"
 "Expected copy-ratio = 0.63663"
 "Mode flag is NA, not generating plots. Sample has failed ABSOLUTE"
When I checked the value of seg.dat[["mode.res"]][["mode.flag"]] in the Rdata file for the failed samples, the reason for failure is stated as "E_CR_SCALE" (the expected copy number was too far away from 1, either <0.75 or >1.25. Check that your seg file is not empty). The segmentation files I am using are generated from Varscan copy number -> DNA copy segmentation programs and they are not empty. These are the raw segmentation results from DNA copy and are not merged or filtered. I am also using maf files with somatic snps called by Mutect.
Can anyone help me understand the reason behind my failed runs. What does capping segs at tCR = 5.0 mean? Is there any parameter that can be adjusted to deal with these samples? Any insight would be great.