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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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get the float copy number values #148

Open hushuzuiniu opened 4 months ago

hushuzuiniu commented 4 months ago

Hi

I have been utilizing your tool for CNV analysis and have found it to be exceptionally useful. However, I have encountered an issue where the copy number values derived from the _ratio.txt files are integers. I am interested in obtaining these values as floating-point numbers for more precise analysis. Could you please guide me on how to modify the settings or process to achieve this?

Additionally, I would like to know if it is possible to calculate tumor purity using this tool.

Thank you for your assistance.

Shu

valeu commented 4 months ago

Dear Shu, the new version that can reliably calculate the tumor purity should be available by the end of August.

For floats, just multiply the median ratio by ploidy.

hushuzuiniu commented 4 months ago

Dear Valeu,

Thank you for your assistance.

I look forward to the updated version of the tool, as it will be of great help. I also have a question regarding the use of floats: should the median ratio be multiplied by a constant ploidy value? Specifically, for human samples, should the median ratio always be multiplied by 2?

Best regards, Shu