Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-18T09:05:32.987Z
Answers.LastActivityDate: 2019-09-18T14:07:05.533Z
Answers.LastEditDate: 2019-09-18T14:07:05.533Z
Answers.UserDisplayName: StupidWolf
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-18T13:10:11.887Z
Answers.LastActivityDate: 2020-06-19T13:12:27.813Z
Answers.LastEditDate: 2020-06-19T13:12:27.813Z
Answers.UserDisplayName: Emily_Ensembl
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-18T13:09:03.010Z
Comments.Text: Please do not cross post to BioStars, Stack Exchange and 1000 Genomes helpdesk as it can create duplicate work:
  https://www.biostars.org/p/399254/
Comments.UserDisplayName: Emily_Ensembl
Tags: <snp><impute2><1000genomes>
Title: 1000 genomes missing SNPs on chr X in GRCh38
ThreadText: # 1000 genomes missing SNPs on chr X in GRCh38
  
  (Asked by: username_0 on 2019-09-18)
  
  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/), [GRCh37](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/).
  
  **Tags:** snp, impute2, 1000genomes
  
  > **Comments:**
  > **username_1**: Please do not cross post to BioStars, Stack Exchange and 1000 Genomes helpdesk as it can create duplicate work: https://www.biostars.org/p/399254/  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2019-09-18. Score: 3 | Accepted answer
  
  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.
  
  
  ---
  
  ### Answer by username_2 on 2019-09-18. Score: 2
  
  I think these are [biallelic snps](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):
  
  > The set is restricted to biallelic SNVs and INDELs.
  
  If you check the [liftover version](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/), the chromosome X is complete...
  
  
  ---
  
  