UCSC very good description of the BED format
Bedtools attempts to auto-detect the file formats used in each command. Thus, as long as your file conform to the format definitions for each file type, you should be okay. For example:
- BAM is zero-based, half-open. SAM is 1-based, closed.
- BED is zero-based, half-open.
zero length intervals (start == end), which in BED format, are interpreted as insertions in the reference.
I can't confirm this but from the top of my head, I recall that
start -1, end in BED format refers to SNPs
(source mostly from BEDTools mailling list)