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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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What is the meaning of suclonal information in the _ratio.txt file #147

Open kmavrommatis opened 4 months ago

kmavrommatis commented 4 months ago

Hi, I am trying to understand what the columns: Subclone_CN and Subclone_Population mean in the file _ratio.txt. I have the following examples from the _ratio.txt file

Chromosome Start Ratio MedianRatio CopyNumber BAF estimatedBAF Genotype UncertaintyOfGT Gene Subclone_CN Subclone_Population
1 925888 0.76209 1.13487 3 -1 2 - -1 1:925887-926116 3 0.773552
1 930204 1.52041 1.13487 3 -1 2 - -1 1:930203-930407 3 0.773552
1 930953 0.895203 1.13487 3 -1 2 - -1 1:930952-931127 3 0.773552

Based on this file the target region 925888.. should have CopyNumber 3 and a subclone with 0.77 CCF (Subclone_Population), correct?

but later in the same segment we have

Chromosome Start Ratio MedianRatio CopyNumber BAF estimatedBAF Genotype UncertaintyOfGT Gene Subclone_CN Subclone_Population
1 945059 0.608181 0 0 -1 2 0 -1 1:945058-945177 3 0.773552
1 945609 0.791256 0 0 -1 2 0 -1 1:945608-945737 3 0.773552
1 946233 2.27771 0 0 1 2 0 -1 1:946232-946399 3 0.773552

where it appears that each of those target regions we have 0 copies, but a subclone with 3 copies and 0.77 CCF. How is this interpreted?

even more confusingly in another region of the genome

Chromosome Start Ratio MedianRatio CopyNumber BAF estimatedBAF Genotype UncertaintyOfGT Gene Subclone_CN Subclone_Population
1 1353187 1.26031 0 0 -1 2 0 -1 1:1353186-1353370 6 0.951405
1 1353532 5.28891 0.808577 2 -1 0.5 AB 23.4944 1:1353531-1353701 6 0.951405
1 1353814 6.26684 0.808577 2 -1 0.5 AB 23.4944 1:1353813-1354327 6 0.951405

These target regions have 2 Copy numbers, but subclone with 6 copies at 0.95 CCF,

How can I interpret these results? Notably the _CNVs file agrees with the CopyNumber column so in these cases I am not sure what we can make out of the Subclone relevant columns.

Thanks in advance for your kind help

valeu commented 4 months ago

Hi, the subclone detection is in Beta.. Unfortunately, I would not trust the results you show. (And generally, something seems to be wrong with the main calls of FREEC. What parameters do you use?)