Question: CNVKit scatter graph will not plot individual chromosomes
0
gravatar for omg what am I doing
6 weeks ago by
Penn State College of Medicine
omg what am I doing60 wrote:

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?

ADD COMMENTlink written 6 weeks ago by omg what am I doing60
1

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.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe45k
1

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
ADD REPLYlink written 6 weeks ago by omg what am I doing60
1

Great, so, all good now?

ADD REPLYlink written 6 weeks ago by Kevin Blighe45k
1

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

ADD REPLYlink written 5 weeks ago by omg what am I doing60
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