The X and Y chromosomes frequently require different analytical approaches as, unlike the autosomes (chromosomes 1-22), they are not present in two copies in all samples. As such, the X and Y chromsomses are not always included in analyses or may be analysed using an alternative methodology.
The pseudoautosomal regions (PARs) are regions of X and Y that share homology. As such, these regions can be amenable to analysis in a similar manner to the autosomes and may be included in analyses where the remainder of these chromsomes are exlcuded.
Analysis of the high-coverage sequencing of the 1000 Genomes Project samples by NYGC has analysed both the X and Y chromosomes in full on GRCh38. Both chromsomes were also analysed by the original 1000 Genomes Project phase three, which analysed data on GRCh37. Full details are in the associated publications, listed alongside the data collections.
Other collections, such as the reanalysis of the original 1000 Genomes Project data realigned to GRCh38, only consider the PAR regions. Again, to understand the work that was done we recommend consulting the publications listed with the data collections.