Simulating with a small sample

[jp-jong]

Hello,

I tried detecting structural variants using minigraph but only by using a toy sample that is 34Mb long. This is chr03 extracted from a rice genome so it's only one "contig". I then used RSVSim to place SVs on it such as:

• 100bp del at 10kb position and 1kb deletion at 1Mb position
• 100bp duplication at 100kb position and 15Mb position.

I used -cxggs to integrate this toy sample w/o SVs + modified toy sample but minigraph did not seem to insert an event or a bubble in this case. See screenshot below.

If all these SVs are in one fasta file, minigraph do not add bubbles but if I create 4 separate fasta files with one of these SVs, minigraph adds bubbles (total of 4). Can someone enlighten me what is happening here? If this is a command error, what is appropriate to add these SVs into a graph? Otherwise, is this a probable bug?

Thanks!