Since GATK 4.5.0.0, HaplotypeCaller now supports custom ploidy regions that can be specified via a new --ploidy-regions argument, overriding the global -ploidy setting: https://newreleases.io/project/github/broadinstitute/gatk/release/4.5.0.0

Similarly, DeepVariant also provides parameters to make the calling aware of the PAR regions in sex chromosomes: https://github.com/google/deepvariant/blob/r1.8/docs/deepvariant-haploid-support.md

DeepVariant is kind enough to provide the PAR BED file directly in the link above. As I understand, the file required by HaplotypeCaller's --ploidy-regions is the non-PAR regions. I am wondering whether I can produce the non-PAR regions by inverting the PAR regions in DeepVariant's PAR BED file.

To be specific, for GRCh38, this is the content of the PAR BED file from DeepVariant download link:

chrX    10000   44821
chrX    94821   133871
chrX    222346  226276
chrX    226351  1949345
chrX    2132994 2137388
chrX    2137488 2781479
chrX    155701383   156030895
chrY    10000   44821
chrY    94821   133871
chrY    222346  226276
chrY    226351  1949345
chrY    2132994 2137388
chrY    2137488 2781479
chrY    56887902    57217415

And I would use it to generate the non-PAR BED file as input for HaplotypeCaller's parameter --ploidy-regions with the following content:

chrX    0   10000   1
chrX    44821   94821   1
chrX    133871  222346  1
chrX    226276  226351  1
chrX    1949345 2132994 1
chrX    2137388 2137488 1
chrX    2781479 155701383   1
chrX    156030895   156040895   1
chrY    0   10000   1
chrY    44821   94821   1
chrY    133871  222346  1
chrY    226276  226351  1
chrY    1949345 2132994 1
chrY    2137388 2137488 1
chrY    2781479 56887902    1
chrY    57217415    57227415    1

Is my logic and the generated non-PAR correct?

I have raised an Issue ticket on GATK's GitHub, but looking at the crazy number of open issues there, I think the possibility is rare that my question gets picked up by the team. So I am trying my luck here.