We provide three genome masks, which were generated according to the three criteria described in the following article: https://www.illumina.com/science/genomics-research/articles/identifying-genomic-regions-with-high-quality-single-nucleotide-.html
These masks define regions of the genome where short-read SNV discovery and genotyping is relatively reliable. The three masks were then intersected to create one combined mask.
Code for producing these masks is provided at https://github.com/arangrhie/T2T-HG002Y/tree/main/accessibility_masks. The following 29 samples were used for the analysis, for consistency with the original work of Bekritsky et al. (link above):
HG00448
HG00449
HG00450
HG01619
HG01620
HG01621
HG01706
HG01707
HG01708
HG01770
HG01771
HG01772
HG02068
HG02069
HG02070
HG02521
HG02522
HG02523
HG02768
HG02770
HG03120
HG03121
HG03122
HG03246
HG03247
HG03248
HG03306
HG03307
HG03308
Also in following with Bekritsky et al., we defined "high quality" bases as those with ≥ 90% aligned reads possessing base quality scores of 20 or more, mean mapping quality scores ≥ 50, and average normalized depth of coverage within 25% of the target (see https://www.illumina.com/science/genomics-research/articles/identifying-genomic-regions-with-high-quality-single-nucleotide-.html for more details).
Thank you to Mitchell A. Bekritsky, Camilla Colombo, and Michael A. Eberle for providing details of their analysis.