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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.

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    $\begingroup$ Please do not cross post to BioStars, Stack Exchange and 1000 Genomes helpdesk as it can create duplicate work: biostars.org/p/399254 $\endgroup$ – Emily_Ensembl Sep 18 '19 at 13:09
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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.

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I think these are biallelic snps:

The set is restricted to biallelic SNVs and INDELs.

If you check the liftover version, the chromosome X is complete...

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