Jon Belyeu

It might help to add the sv type to the plot command with the `-t INV`. That'll expand the window and show the breakpoints where the SV was called. The...

`samplot vcf` is struggling to connect the samples in your VCF with the bam you included, a challenge when dealing with multiple bams. Check out the `--sample_ids` argument in the...

Hmm, hard to say. Try running again with the `--debug` option. That will output a message for most skipped variants explaining why they were skipped. Is it possible that there...

Looks like the majority of the variants were excluded by the important_regions bed file. Maybe a good idea to test without that option to see what happens? It's possible that...

Well, it looks like multiple filters are omitting variants. - You have a large number of what appear to be small/single-ended BNDs and insertions, neither of which is supported by...

This issue is a bit out of scope, relating perhaps more to IGV than to samplot SV review. However, you could clone/fork this repository and add a print statement in...

Hey, thanks for pointing this out. We'll improve handling for this situation where the region is so small. However, samplot doesn't support insertions because they only exist at one reference...

The orange indicates a long read and the color-coding shows what type of structural event the CIGAR operation supports. Blue is an inverted alignment, dark grey is a deletion, and...

A note on the `samplot vcf` issue: I've noticed some issues with, for example, slightly malformatted VCF files that caused silent failure. To troubleshoot, try out the `--debug option`, which...

Glad you like it! The location of the arrows has been a tough decision. We decided to place them at the far right to decrease overplotting, which becomes a more...