I've found something unexpected, may be I just didn't understand how coordinates work.
I am intersecting a bed file with coordinates:
1 100 101
Against a vcf file, which has two sites in it:
1 100 etc etc 1 101 etc etc
The bed coordinates define a single site (100 in zero-based or 101 in one-based) However, intersectBed says that this bed line intersects with both vcf lines. I thought it should only intersect with 1:101 (vcf is 1-based). Isn't that incorrect? What am I missing?