This is so interesting, I have this issue with bedtools, and I spent hours trying to figure out the all the mismatches. Thank you for the tips.
1/ Your bedtools intersect returned zero results. You stared at the screen for 20 minutes.View quoted post on X
The BED file looked fine. The command was correct. Everything should have worked.
I've debugged this exact problem hundreds of times. It's almost always one of these 4 traps:
