Heatmap interpretation

[ethering]

Hi,
Below is my heat plot generated using Sniffles2_plot.
I generated seven .snf files with Sniffles, and then did joint SV genotyping using the seven .snf files to create a single multi-sample VCF file of SVs.
There are a couple of things that I don't understand (or that don't make sense).

1. The legend states that brown refers to zero shared insertions or deletions. When the same samples are compared (the brown diagonal of squares across the plot), surely all insertions and deletions are shared so these squares should be closer to deep purple and not brown?
2. In my dataset, my first sample (C1...) has 126,118 insertions, but the legend only goes up to around 9,000. Why is this?

[farhangus]

Hi,
Thanks fo ryour message. The diagonal cells, which are brown, indicate that we are not showing the shared variants between the samples and themselves. Instead, we are showing the shared variants for each sample compared to others. For example, the right side shows the number of shared variants for C1 versus all other samples. Please let me know if you need anything else.