How to get the "Genotype" for input files? about quantumclone HOT 3 CLOSED

Hello,

1 & 2. A & B are the major and minor allele respectively. So a genotype AB is what you expect for normal cells. AA means loss of heterozygosity, ....
3. From the previous answer, only AAAA, AAAB and AABB are possible at the 4 copy level
4. They should all be A
5. 0 copy should mean that the portion has been deleted except for non-cancer cells
6. In the publication we used FREEC ( http://boevalab.com/FREEC/ ). I guess that there are now numerous possibilities to do so. It should also provide and estimate of purity to correct for contamination by normal cells in the samples.

Hope this helps.
Best wishes,
Paul DEVEAU

from quantumclone.

Thanks a lot @DeveauP !

Forgive me for one more question:
Do you have any suggestion about the software to estimate purity ?

from quantumclone.

Delayed answer here.

We originally estimated the purity with Control-FREEC, I don't know what is SOTA currently.

from quantumclone.