Closed mariaalexandrastanciu closed 10 months ago
Hi @mariaalexandrastanciu,
For NRH15001, it seems like your BAF track corresponds to the logR track, can you double-check the parameter you use when running the ascat.loadData
function?
The logR for normal will always be a flat line at 0, that's expected. I'm not sure what happens for your sample NRH30008 but the logR is so noisy that it should be discarded. Does it have a lower coverage (or its matched normal) or anything particular? Is the reference genome (hg19/38) the same for your entire batch?
Cheers,
Tom.
Hi Tom,
Thank you very much for your fast reply. I was indeed messing with loadData parameters.
For the NRH30008 sample, I do have lower coverage, 35x, compared with most of my samples. Do you have any suggestion on running ASCAT on this sample, or you would advise to discard it ?
Bests, Alexandra
Hi @mariaalexandrastanciu,
Could you please share the ASPCF plot for this sample? It could be the segmentation went fine (even though the raw data is extremely noisy). If it's also very noisy, I recommend you try our ASCAT.sc tool (https://github.com/VanLoo-lab/ASCAT.sc) which leverages off-target reads to derive copy-numbers. This may help in getting a clean CNA profile.
Cheers,
Tom.
Hi,
Here it is:
Bests, Alexandra
Hi @mariaalexandrastanciu,
Yep, it's very noisy and there aren't many options I'm afraid. ASCAT.sc may be able to help here, but you should not consider the output from ASCAT.
Cheers,
Tom.
Ok, I see.
Thanks a lot for your input!
Bests, Alexandra
Hi,
It seems that I ran into this problem for most of my WES samples(~80). I have the normal WES as well and the coverage is around 250 for tumor samples and 100 for normal samples.
I believe that the BAF is looking strange, but I don't know what can be the issue.
Here is an example after correction: Tumor LogR/BAF:
and
Normal LogR/BAF:![After_correction_NRH15001 germline](https://github.com/VanLoo-lab/ascat/assets/31191087/096ba512-903b-4274-a732-fecfb2a83561)
Can you give any suggestion on what is happening? I do have some samples for which I have purity/ploidy, but they as well look weird:
Tumor after correction:![After_correction_NRH30008 tumour](https://github.com/VanLoo-lab/ascat/assets/31191087/8daeb223-9972-476f-a40d-51dd2eade6bd)
Normal after correction:![After_correction_NRH30008 germline](https://github.com/VanLoo-lab/ascat/assets/31191087/2dbb8bc2-657f-482b-b8d9-7a582d5e3bd3)
Thank you, Alexandra