<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>

CC BY-SA 4.0
2019-09-18T09:05:32.987Z
2019-09-18T14:07:05.533Z
2019-09-18T14:07:05.533Z
StupidWolf
<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>

CC BY-SA 4.0
2019-09-18T13:10:11.887Z
2020-06-19T13:12:27.813Z
2020-06-19T13:12:27.813Z
Emily_Ensembl
<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>

CC BY-SA 4.0
2019-09-18T13:09:03.010Z
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/
Emily_Ensembl
<snp><impute2><1000genomes>
1000 genomes missing SNPs on chr X in GRCh38
# 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/  

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## 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.


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### 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...


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