Subclones output file

[kathryn-beal]

Hi,
A scientist in our group has found a case where the cellular fraction (frac2_A) of the nMaj2_A and nMin2_A columns has a higher value than frac1_A from the callSubclones subroutine (version 2.2.5). We would be very grateful if you could explain why this is the case.

For example:

zcat subclones.txt.gz | awk 'BEGIN{ FS=OFS="\t" }{ print $1,$2,$3,$8,$9,$10,$11,$12,$13 }' | column -t | less -S
chr startpos endpos nMaj1_A nMin1_A frac1_A nMaj2_A nMin2_A frac2_A
...
12 19462666 19698320 3 0 0.381011741894733 3 1 0.618988258105267
...
12 37866866 83372701 2 1 0.431746072237525 3 1 0.568253927762475
...
12 83501125 133836024 2 0 0.332939966391955 2 1 0.667060033608045
...

Are these fractions supposed to be listed with major fraction on the left and minor fraction on the right, which is not what we are seeing here?
Regards
Kathryn

[sdentro]

Hi Kathryn,

The solutions are not sorted by the proportion of tumour cells estimates. So it's entirely possible for the larger proportion to be mentioned second, there is no special meaning.

Best,
Stefan