Draw centromere on chromosome scatter plot

Question

[Hällyss]

Hello,

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

Alice

Answer 1

[Eric T.]

When CNVkit segments your .cnr file with the CBS algorithm, it automatically finds the largest no-coverage gap in each chromosome, i.e. the centromere, and segments each arm of the chromosome separately. This will be visible in diagram and the genome-wide or chromosome-level scatter plots. Is any of this not working for you?

If you want to plot each arm of a chromosome separately and you know the coordinates of the centromere, you can use scatter -c to specify the coordinates of the chromosome arm:

cnvkit.py scatter sample.cnr -s sample.cnr -c chr9:1-48000000 -o sample-chr9p.pdf

If you just want to add a vertical line to the middle of the chromosome-wide plot, you can do this either in Python using cnvlib.do_scatter and matplotlib, or else edit the original PDF in Inkscape.