Plotting alternate solutions, segments, and other outputs.

[teacakedeadlift]

Running ichorCNA as a container on early disease samples with low TFx. The outputs it generates are presumably all relating to the selected most likely solution (all the _CNA_chr.pdf files and all the *.cna.seg, *.seg, and *.seg.txt). However, as per the wiki solutions around the 0.03 - 0.1 should be checked if large areas are being called as CNAs - i.e. whole arms etc. When doing this it appears that other solutions may be more reasonable.

I am trying to establish if these are likely true positives by comparing .seg files in IGV versus paired tissue samples. This does not work if the .seg only represents one of the possible solutions.

Is there a way to produce corresponding files for all of the solutions so that I can then select the best .seg file for further analysis? Assume I would use plotting.R but unsure exactly how.

Thanks

Phil