I am running CNVKit 0.9.6 and I cannot get the scatter function to plot an individual chromosome. It will generate a PNG of all chromosomes but I cannot display just one using:
cnvkit.py scatter 27s.cnr -s 27s.calls.cns -c chr9 -o 27s_scatter_chr9.png
I get an error:
ValueError: No usable data points to plot out of 0 probes, 0 segments, 0 variants
But there are clearly datapoints on the chromosome in the scatterplot of all chromosomes. Has anybody encountered this before? An error on my end or a bug?