1000 genomes missing SNPs on chr X in GRCh38 I am trying to get a reference together for imputation using the 1000 genomes data set. The GRCh38 version of the data set was made available earlier this year, but seems to be missing a significant number of SNPs on the X chromosome (~96%).

Is there any resource that can explain why? I have tried searching on their home page with no luck.

The data sets in question are GRCh38, GRCh37.
As I told you on 1000 genomes helpdesk:
Because of the ploidy settings we used for our variant calling, we only called variants in the the pseudoautosomal region on the X chromosome. We are working on settings to correctly analyse X variants in both males and females and plan to analyse X properly soon.