1-based coordinate system
A coordinate system where the first base of a sequence is one. In this
coordinate system, a region is specied by a closed interval. For example, the region between
the 3rd and the 7th bases inclusive is [3; 7]. The SAM, GFF and Wiggle formats are using the
1-based coordinate system.
Other:
GTF, Blast default output

VCF

0-based coordinate system
A coordinate system where the first base of a sequence is zero. In this
coordinate system, a region is specied by a half-closed-half-open interval. For example, the
region between the 3rd and the 7th bases inclusive is [2; 7). The BAM, BED, and PSL formats
are using the 0-based coordinate system.