Missing sub clones

[jfwise]

I ran the python command and for some reason from the branches and CNV_Files there is no information for some sub clones. For example the unique sub clone names from cell groupings was
[1] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.1.1.1"
[2] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.1.1.2"
[3] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.1.2.1"
[4] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.1.2.2"
[5] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.2.1.1"
[6] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.2.1.2"
[7] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.2.2.1"
[8] "malignant_HPT1Pat1.malignant_HPT1Pat1.1.2.2.2"

but in the CNV_files there is only
1,0.0
1.1,0.0,B
1.1.1,50.25716385011021,C
1.1.2,5.6208670095518,D
1.2,0.0,E
1.2.1,9.184423218221896,F
1.2.2,34.937545922116094,G

There never seems to cluster names with all four digits.

[saikatds-bd]

Hi! I know it is too late and probably you have already sorted it out, but writing it for others from my experience (and also to know if I misunderstood anything). I think the missing subclones are due to the threshold set in the uphyloplot2 python script. For example, I got less subclones in the uphyloplot2 output when I used "python uphyloplot2.py -c 10", even less by "python uphyloplot2.py -c 15" and so on. The default is set to 5 (Only subclones that comprise at least 5% of cells will be included for plotting), so it will filter out some subclones (as we see in our input .cell_groupings file) even if we do not set a threshold ourselves.

[mluciarr]

I had the same problem and I run it with the python uphyloplot2.py -c 0 and all the subclones appear properly.