CNVkit result interpretation

Question

[enes]

Hi everyone, I am trying to make copy number variant analysis with CNVkit tool.

I applied the standard procedure to find copy number variants.

-target bed -antitarget bed -generate referance cnn -autobin -target coverage -antitarget coverage -fix -segment -calling

After these standard steps, I make a diagram plot with using calling step output data.

According to this plot, the entire X chromosome has been deleted. How can this be?

After that I checked to CNS data to understand what happened.

ChrX range is really huge and weight value is high? what do you think about this result guys? If the X chromosome were indeed deleted, the patient would have died long ago...

[brunobsouzaa]

One thing I like to do is to perform call on cnr files instead of cns files. This will split your segments into regions. Also, check for you ploidy parameters. Like biobiu answer, it seems that you're dealing with a male sample against a female reference.

Answer 1

[biobiu]

I guess you should tune the ploidiy parameters... It seems that this is a male sample analyzed against female/mixed reference