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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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Clarification of a neutral CNV #115

Open vucinick opened 1 year ago

vucinick commented 1 year ago

Hi,

I couldn't find anywhere what does status (type of alteration) neutral mean in a CNV file? Why is it reported? If an organism is diploid, and I get CNV of 2, I would expect that's normal. Should I just ignore the ones that have CN normal? My datatable looks like this: image

Control-FREEC (v11.6) was run as a part of NF-core pipeline sarek.

dmasoodfda commented 1 year ago

Hello!

The neutral alteration could be special case of LOH where the alteration does not result in a loss of copy number.

I was also wondering if you could share your config file as well. I am having a lot of trouble in getting the LOH calling to run and obtaining the 'somatic.germline' column as you have. I just want to see which parameters should be set and what SNP file you are using to get this to run effectively.

thanks Daniall

vucinick commented 1 year ago

Hi Daniall,

Thank you for your response! After the closer inspection, yes it was LOH events, thank you :)

Here is the config file used in the nf-core Sarek pipeline: Control-FREEC.config.txt.

Cheers, Kim