File chm13v2.cen-mask.bed gives the approximate locations of centromeric satellite repeats and acrocentric short arms in CHM13 v2.0. It was manually constructed based on the official satellite annotation, the DNA-BRNN satellite annotation and the minigraph pangenome graph from the HPRC year-1 data. Alignment in the BED regions is usually much worse than in the rest of the genome. This file is intended for filtering spurious alignments or variant calls caused by centromeric repeats.

File hs38.cen-mask.bed was constructed similarly from DNA-BRNN annotation and regions where minigraph alignment faded.

These files are also available on Zenodo.