CNV calling with bams with only chrY region

[subinieee]

Hello,

I'm currently using CNVkit for calling germline CNVs in Y chromosomes using WGS data.
For my input bams, I extracted chrY region of WGS data using samtools and converted into .bam format.
I have also added a target bed file (-t) only to cover chrY regions.
The tool runs fine although it returns a log message 'No chrX found in sample; is the input truncated?' as there is no chrX data.
I was wondering if missing chrX or other autosomal regions in input affects the log2 ratio calculation?

Thank you!
Subin