Is ichoCNA used only for tumor-normal mode?

broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

GNU General Public License v3.0

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Is ichoCNA used only for tumor-normal mode? #78

Open ArshiyaG opened 4 years ago

ArshiyaG commented 4 years ago

Is ichorCNA used only for tumor-normal mode or tumor only mode? Because I get a very low tumor fraction value when run with a tumor only liquid biopsy sample and a higher value when run with tumor-normal mode

Thanks in advance Arshiya

gavinha commented 4 years ago

Hi @ArshiyaG

ichorCNA can be used for tumor-only mode. I am not able to comment on your issue without additional information.

Best, Gavin

ArshiyaG commented 4 years ago

Hi @gavinha

I ran ichorCNA for noth tumor-normal and tumor-only file. Tumor fraction I got for Tumor-only mode was very low compared to Tumor-normal mode. So Is ichorCNA not compatible with tumor only mode?

Thanks in Advance Arshiya

gavinha commented 3 years ago

Hi @ArshiyaG

ichorCNA runs on tumor-only mode by default. Of course, including a normal sample will improve the analysis. There are several reasons for discrepancies between tumor-normal vs tumor-only. The first obvious reason I can think is the ploidy estimation. I won't know for sure unless I see your results.

Best, Gavin