Topic
0-based vs 1-based coordinates
Is this file 0-based or 1-based, and am I off by one?
BED is 0-based half-open; GTF, GFF, VCF and SAM are 1-based closed. Converting between them without adjusting the start coordinate shifts every feature by one base, which is invisible in a genome browser and fatal for SNP annotation and motif analysis.
- How to Avoid 0-Based vs 1-Based Coordinate Errors in Variant Calling
A VCF position and a BED start are not the same number, and the mismatch silently drops the first base of every target interval.