Open JD12138 opened 1 year ago
Hi @JD12138,
The steps leading to sample.call.cns
file are not vey well documented :
sample.cns
file) are filtered to remove likely false-positive segments (based on confidence interval calculation)To sum up your observed CN and log2ratio values are not inconsistent
=> Everytime a log2ratio falls between -0.25 and 0.2, called CN is "neutral" = reference ploidy = 2 (by default)
=> Your first row with log2ratio=0.224267 is above 0.2 threshold so CN=3 is called
Hope this helped ! Have a nice day, Felix.
Hi, I recently updated CNVkit (i used 0.9.5 for a looong time) and noticed that batch
produces also call.cns
files with p_ttest
column and without ci_hi / ci_lo
columns. However, when I manually calculate call.cns
files, the latter are preserved while p_ttest is not calculated. I wanted to ask whether pval can be calculated here using some bulit-in command of function or only manually from confidence intervals?
Hello, I have a pair of WGS sample (A normal and a tumor). And I use the command line to detect CNVs. cnvkit.py batch $tumor --normal $normal \ --fasta $reference \ --annotate $refFlat \ --output-dir $out/$sample \ -p 20 -m wgs \ --scatter --diagram
But the log2Ratio and the copy number in my sample.call.cns file is inconsistent. I list the top 10 lines below: log2 cn 0.224267 3 -0.207029 2 0.0982319 2 -0.222901 2 0.140716 2 -0.117483 2 0.0339522 2 -0.0921905 2 0.157111 2
Could you tell me the reason? Or what's the defination of log2Ratio and cn in this file ? Thank you!