Traditionally, genomic positions are represented in cytogenetics as ‘Cytogenetic Bands’, regions of chromosomes that vary in the density with which they stain with the Giemsa dye. These references come in the format
[chromsome][arm][band] - for example,
9q21.3 would represent band
21.3 on the
q arm of chromosome
These references don’t always play well with the genomic base pair coordinates that are now commonplace with the sequencing of the human (and many other) genomes.
Converting one to the other is a tedious task, so I put together a script to automate the task. It’s available to use online here.
The script takes an input of either cytogenetic bands or chromsomal coordinates, and converts the input into the other format. It’s written in perl, and I’ll release a download for command line use here soon. It works by cross-referencing a cytogenetic map (an ideogram) provided by the UCSC.