One-based – The start position for a sequence when chromosome numbering starts at 1. This position provides the actual location of the nucleotide.
Zero-based – The start position for a sequence when chromosome numbering starts at 0. This position provides the location of the flanking nucleotide.
Fully closed – Closed start, closed end, including both endpoints
Fully open – Open start, open end, excluding both endpoints
Half-open – Closed start, open end, includes the first endpoint but not the last endpoint.
The coordinate system is described in details by this UCSC article.
Important: When entering Region targets in Designer, the input should be one-based.
All .bed files store the coordinates in zero-based, half open system. This applies to these Tapestri Designer output files:
These files are one-based, fully closed:
The reason for this is that .csv, .amplicons, and .gatk files are designed to be human-readable, so having the one-based format is easier for users to understand.
The .bed files are used for computation, so they are zero-based, which reduces computation as mentioned on the UCSC link.