Closed albamasmalavila closed 11 months ago
Hello,
I have run Ascat in several samples and it all seems to have run correctly except for 1 sample out of 12, from which I got this warning:
"ASCAT could not find an optimal ploidy and purity value for sample X"
I've checked the logR and BAF plots and they don't look good. I attach here the plots after GC and RT correction:
![PDX_08_P0_vs_PRO238 after_correction_gc_rt PDX_08_P0_vs_PRO238 tumour germline](https://github.com/VanLoo-l ab/ascat/assets/71131635/7386be1d-ca8c-4c10-b68c-d0f7caff807f)
Do you know what might be the problem with this sample and if there is a way to calculate the ploidy and purity in such cases? It should be similar to the other samples, which have a tumor fraction around 1 and a ploidy between 1.9 and 3.8.
Thank you very much,
Alba
Hi @albamasmalavila,
It is very likely that this sample has a really low coverage. If that's the case, nothing can be done but to exclude it.
Cheers,
Tom.
OK, thanks for your reply.
Hello,
I have run Ascat in several samples and it all seems to have run correctly except for 1 sample out of 12, from which I got this warning:
"ASCAT could not find an optimal ploidy and purity value for sample X"
I've checked the logR and BAF plots and they don't look good. I attach here the plots after GC and RT correction:
![PDX_08_P0_vs_PRO238 after_correction_gc_rt PDX_08_P0_vs_PRO238 tumour germline](https://github.com/VanLoo-l
ab/ascat/assets/71131635/7386be1d-ca8c-4c10-b68c-d0f7caff807f)
Do you know what might be the problem with this sample and if there is a way to calculate the ploidy and purity in such cases? It should be similar to the other samples, which have a tumor fraction around 1 and a ploidy between 1.9 and 3.8.
Thank you very much,
Alba