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: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/