[Bioc-devel] Cytogenetic bands

Ilari Scheinin ilari.scheinin at gmail.com
Sat Mar 22 18:12:56 CET 2014


I would like to obtain the boundaries of cytogenetic bands for human (hg19) as I need to map arbitrary genomic positions to the band containing them. I figured these would be available via the Homo.sapiens annotation package, so I took a look at the available keytypes. MAP looked promising:

> library(Homo.sapiens)
> head(keys(Homo.sapiens, keytype="MAP"))
[1] "19q13.4"  "12p13.31" "8p22"     "14q32.1"  "3q25.1"   “2q35”

However, upon a closer look, these don’t appear to be the actual bands themselves, but are instead the matching bands for some other level of data, as it contains entries such as "19q13-qter”. (And there are 2,446 of these entries whereas there are 862 bands.)

A bit of searching returned two software packages that do contain this information: idiogram (data(Hs.cytoband)) and OmicCircos (data(UCSC.hg19.chr)). The first one seems to be from genome build hg17, but the second one has hg18 and hg19. However, using a software package instead of an annotation one to obtain this information seems wrong, and makes me worry if it will be kept up-to-date in the future (c.f. idiogram).

So, are the coordinates of the cytogenetic bands contained somewhere in the annotation packages?


More information about the Bioc-devel mailing list