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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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Interpreting an increase in CN for the majority of the genome #80

Open haraldgrove opened 3 years ago

haraldgrove commented 3 years ago

I've just analaysed a WGS dataset (matched tumor-normal) from a breast cancer sample and the output is telling me that most of the genome is noted as having an increase in copy numbers (CN=3). (see figure of Ratio*2 below)

I just wanted to know if there might be an issue with the normalisation and that the real result should have been mostly normal regions with some regions having a reduction in copy number instead?

Thank you

WGS_BB-T0040-DNA cnv

valeu commented 3 years ago

Dear Harald, it depends on whether you used the [BAF] option or not. If you used it, then FREEC will likely assign CN=3 correctly. Did you look at the resulting BAF?

haraldgrove commented 3 years ago

I did not use any of the BAF options. I can try and add those and see what happens.

Thanks.

valeu commented 3 years ago

Yes, please share then the second graph with BAF values to be sure that it worked!

haraldgrove commented 3 years ago

I re-did the analysis with BAF, and the CN-values changed for several of the sections. I'd assume that this is then a more correct view of the CNVs.

WGS_BB-T0040-DNA cnv

valeu commented 3 years ago

You should also visualize the BAF info. Does it make sense?

haraldgrove commented 3 years ago

I'm not sure if I can say it makes sense or not. The BAF matches the other results, but I don't know how it would look if there was anything wrong.

BB-T0040-DNA_recal bam_BAF txt

valeu commented 3 years ago

It fits! But I will update the visualization script written 10 years ago to make things more readable.