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VanLoo-lab / ascat

ASCAT R package
https://www.mdanderson.org/research/departments-labs-institutes/labs/van-loo-laboratory/resources.html#ASCAT
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Could not find optimal ploidy and purity #160

Closed albamasmalavila closed 11 months ago

albamasmalavila commented 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 PDX_08_P0_vs_PRO238 after_correction_gc_rt PDX_08_P0_vs_PRO238 tumour tumour 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

tlesluyes commented 11 months ago

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.

albamasmalavila commented 11 months ago

OK, thanks for your reply.

Cheers,

Alba