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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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No normalization although it is requested #144

Closed s-juross closed 4 months ago

s-juross commented 4 months ago

I'm running ControlFREEC with targed NGS data and no control data and in order to normalize I attempted to run the specified on the website I generated a GC-content profile with gccount. But even with this specified in the config file, ControlFREEC doesn't normalize either with the GC-content nor with the mappability profile. Does somebody have an idea what the problem is? I've attached the config file. CNV_config.txt Am I right that CNVs without normalization are basically useless?

valeu commented 4 months ago

Hi, I franckly don't think that it makes sense to try to call CNA on targeted sequencing data without controls: the capture bias is very strong. I suggest the OncoCNV tool for amplicon panels - there one can use many unmatched samples as controls.

s-juross commented 4 months ago

Thank you for the answer!