Warning when running Samplot vcf

[MeHelmy]

Used command
samplot vcf -v SV.sort.vcf -O png -b data.bam --important_regions gene_region.bed -d results --sample_ids "data.bam" --gff Homo_sapiens.GRCh38.100.chr.gff3.chr.gz --command_file   samplot_commands.sh

I have results (but the gff annotations are not shown), the region should contain 7 DEL and 5 INS, only 6 deletions exist in the index.html file.

There is this warning:

samplot.py:2951: UserWarning: FixedFormatter should only be used together with FixedLocator
  curr_ax.set_xticklabels(labels, fontsize=xaxis_label_fontsize)

[jbelyeu]

There are a number of default filtering options in samplot vcf which remove some SVs. The optional flag --debug can be added to your command and will print the reason each skipped variant is skipped. INS variants are unfortunately not supported by samplot because the signals it shows (depth of coverage, split/disordant pairs) don't work well for either novel insertions or mobile elements.

Regarding the GFF, just to verify, you're certain there are GFF annotations for the regions plotted? If so, something is wrong and I'm happy to dig into it.