Copy Number Variants with CNVKit
Hi everyone, hope yall doing well.
I'm actually on a project working with CNVKit to analyze copy number variant from somatic NGS data of heterogen tumor (cfDNA = Circulant Free DNA). In my analysis I've specified the option :
cnvkit.py call "$SAMPLE_DIR/${SAMPLE}.cns" --method threshold \
-t=-0.20,0.20 -o "$SAMPLE_DIR/${SAMPLE}.called.cns"
I would like to know if there's any document or idea that could help to adjust the thresholds with the -t option for the Log2_Ratio.
Instead of using the default one :
-t= -1.1,-0.25,0.2,0.7 .
Thank you in advance.
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