I run CNVkit with my somatic data. I draw scatter plot, of the chromosomes. Sometimes the segment is very long and I think there is maybe du to a CNV in a arm of a chromosome. So I want to separate the different arms of a chromosome in my plot. My idea is to show the centromere of the chromosome.
cnvkit.py scatter sample.cnr -s sample.cns -g centromere_chr1 -c chr1 -o sample_chr1.pdf
So I add the genomic region of centromer of each chromosome in my bed. I ran the analyse and I try to plot the chromosome.
I have an error. cnvkit explain me that the region "centromere_chr1" does not exist. I understand in the fix step, the regions of target with no coverage (here centromere) are filtred.
Is it possible to get around this problem (only mark the regions with no coverage for exemple) ?
Thank you for your answer