text: user6225: 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.
  
  user5077: 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...
  
  user1332: 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.
  
original_text: 6225: <p>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%).</p>
  
  <p>Is there any resource that can explain why? I have tried searching on their home page with no luck.</p>
  
  <p>The data sets in question are <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/" rel="nofollow noreferrer">GRCh38</a>, <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" rel="nofollow noreferrer">GRCh37</a>.</p>
   5077: <p>I think these are <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/20190312_biallelic_SNV_and_INDEL_README.txt" rel="nofollow noreferrer">biallelic snps</a>:</p>
  
  <blockquote>
    <p>The set is restricted to biallelic SNVs and INDELs.</p>
  </blockquote>
  
  <p>If you check the <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/" rel="nofollow noreferrer">liftover version</a>, the chromosome X is complete...</p>
   1332: <p>As I told you on 1000 genomes helpdesk:<br />
  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.</p>
  