Genomic Coordinates

When to use

Any time a coordinate crosses a boundary: between two file formats, between two tools, between two assemblies, or between the genome and a transcript.

The rule

A coordinate is three facts, not one: the number, the convention it is written in, and the assembly it was measured against. Carry all three or the number is not interpretable.

Coordinate errors are the quietest class of bug in genomics. An off-by-one BED file parses, sorts, and intersects without complaint. A GRCh37 VCF joined against a GRCh38 annotation returns rows. A right-shifted indel simply fails to match its entry in ClinVar, and the result is a variant reported as novel. Nothing raises an error; the answer is just wrong, and it is wrong in a direction that looks plausible.