Hi all! If you could help me on this issue I'd really appreciate, thanks in advance!

Hi @Elisabet Figuerola maybe someone in the community has experience with ASCETS but we don't since we get the CN levels directly from the OA output. The tools you might want to look into next to PURPLE are the COBALT outputs and the LINX copy number output ".linx.vis_copy_number.tsv", these have bin and arm level copynumbers and BAF information in an easy to access format.

And the latest version of OA (I'm running 2.3, the esvee-xmod branch from @Rayan Hassaïne) contains a

".purple.chromosome_arm.tsv"

file which might achieve exactly what's needed:

chromosome	arm	meanCopyNumber	medianCopyNumber	minCopyNumber	maxCopyNumber
1	P	1.9339	1.9976	1.0345	6.2549
1	Q	2.0095	2.0116	1.9802	2.0116
2	P	1.9960	1.9965	1.9916	2.9393
2	Q	1.9956	1.9956	1.9956	1.9956
3	P	0.9967	0.9950	0.9950	2.8627
3	Q	2.6619	2.0846	1.0174	16.2368
4	P	1.9859	1.9859	1.9859	1.9859
4	Q	1.9629	1.9596	1.9596	7.9458
5	P	1.9509	1.9447	1.9447	1.9626

Thanks Joep and Jose for the feedback! I wasn't sure if my interpretation on the bafCount column in Purple file

.purple.cnv.somatic.tsv

(refered as the Count of AMBER baf points covered by this segment) was equiparable to the number_of_markers column from ASCETS, which is the per-segment count of probes/targets used to define that CNV segment.

Yes you can consider those equivelant (with the small note they use different probe sets so numbers are not 1-to-1 comparable)