CNVKit scatter graph will not plot individual chromosomes

Question

[Getting there]

Hello,

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?

[Kevin Blighe]

Calling Eric T.

omg what am I doing, have you verified that you actually have a contig named 'chr9' in your data?; do all of your contigs have a 'chr' prefix? Are there other thresholds of the scatter function that mean that no regions in your data are being plotted? - perhaps check the manual pages.

[Getting there]

Thank you, I forgot I had removed the chr prefixes in my analysis. That resolved the error but I got a different error

IndexError: indices are out-of-bounds

Apparently this was an issue that was fixed in 0.9.6 according to this thread scatter plots with single chromosome gives IndexError but it still showed up for me. The fix joseph.fass suggested, to add chromosome bounds seemed to fix it however.

CNVKit_DRAGEN_BAMs]$ cnvkit.py scatter 27s.cnr -s 27s.calls.cns -c 9:1-141213431 -o 27s_scatter_chr9.png

[Kevin Blighe]

Great, so, all good now?

[Getting there]

Yes, seems to work fine with the chromosome bounds specified.