So far, CNV histograms and .pgxseg segment and matrix files used a 1Mb genome binning, based on the consecutive assignment of 1Mb intervals from 1pter -> Yqter. This resulted in 3102 intervals, with the last interval of each chromosome being smaller.
On 2022-02-11 we have changed the procedure. Now, the last interval of the short arm of any chromosome is terminated at the centromere, leading to
Also, since a few qter intervals were very small we now use a padding factor (currently 100000 bases) to determine if the last band would be smaller - in which case it is discarded and the previous interval extended to cover up to the telomere. This applies to chromosomes 6 and X, where the last intervals become now slightly larger than 1Mb:
Since many CNVs have natural breakpoints at chromosomal centromeres the new interval mapping should provide a better representation of genomic events. Also, such a mapping facilitates the calculation of e.g. arm specific CNV fractions which are sometimes used as statistical indicators. Enjoy!
@mbaudis 2022-02-11: more ...