State a genomic coordinate with its assembly, contig naming, and coordinate system.
The move: never separate a coordinate from its reference. A genomic coordinate needs a contract. The minimum contract is assembly, contig name, and coordinate convention. Assembly tells you which reference sequence set is being used. Contig name tells tools which sequence inside that assembly to use. Coordinate convention tells you how to interpret the numbers. This matters because bioinformatics formats do not all use the same coordinate logic. VCF positions are commonly read as 1-based positions. BED intervals are commonly 0-based half-open intervals. SAM records include a 1-based leftmost mapping position, while BAM indexing introduces other coordinate details. A result…
Sign up free — one personalized lesson every day, matched to your role and goals.
Already have an account? Sign in