Answers.Body: <p>Sounds like you're looking for the <a href="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi" rel="nofollow noreferrer">dbSNp</a> files. You haven't specified a species, but you can download the data for human from the <a href="https://ftp.ncbi.nlm.nih.gov/snp/" rel="nofollow noreferrer">dbSNP FTP site</a>. Specifically, you want:</p>
  <pre><code>wget https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
  </code></pre>
  <p>This file has lines like:</p>
  <pre><code>1   10848   rs1271898990    C   G   .   .   RS=1271898990;RSPOS=10848;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99998407237512742,0.00001592762487257
  1   10851   rs1340958514    G   A   .   .   RS=1340958514;RSPOS=10851;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99996018093781855,0.00003981906218144
  1   10854   rs1222740568    G   A,C .   .   RS=1222740568;RSPOS=10854;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99967348369011213,0.00019113149847094,0.00013538481141692
  1   10857   rs1487378566    C   G   .   .   RS=1487378566;RSPOS=10857;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99933900356778797,0.00066099643221202
  </code></pre>
  <p>However, it sounds like you might be underestimating the complexity here. There isn't just one minor allele, many sites have multiple minor alleles. The example above shows one such multiallelic site (you can split these into separate lines using <code>bcftools</code>). But you also have cases like:</p>
  <pre><code>1   10786   rs1464509424    CGGCGCA C   .   .   RS=1464509424;RSPOS=10787;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP;TOPMED=0.99991239806320081,0.00008760193679918
  1   10786   rs1258377526    CGGCGCAGGCGCAGACACATGCTAGCGCGTCGGGGTGGAGGCGT    C   .   .   RS=1258377526;RSPOS=10787;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP
  </code></pre>
  <p>Don't expect just one major and one minor allele per location.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-10T18:22:11.047Z
Answers.Text: This is probably it, thanks. I looked on the dbSNP website but couldn't find the exact right file. I have a good method in place for handing multiallelic sites
Answers.UserDisplayName: BigMistake
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-10T07:10:35.107Z
Answers.LastActivityDate: 2023-10-10T07:10:35.107Z
Answers.UserDisplayName: terdon
Answers.Body: <p>I agree with @terdon that perhaps dbSNP is what you may want to look at. The dbSNP155 RefSNP VCF file in GRCh37 version may help. It can be downloaded from <a href="https://ftp.ncbi.nlm.nih.gov/snp/latest_release/vcf/GCF_000001405.25.gz" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/snp/latest_release/vcf/GCF_000001405.25.gz</a>.</p>
  <p>You may also fine the 1000G genome website helpful. <a href="https://www.internationalgenome.org/data-portal/data-collection" rel="nofollow noreferrer">https://www.internationalgenome.org/data-portal/data-collection</a> contains much of its release both in <code>.fa</code> format and in VCF format. I understand that a large number of samples included increase the file size tremendously, but it is necessary as you're not just looking at what the major and minor allele is, but also their frequency, which may vary greatly between populations. It's important to check which population we're seeing when using their genomic information.</p>
  <p>Hope my answer helps. Regards.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-20T16:58:11.767Z
Answers.LastActivityDate: 2023-10-20T16:58:11.767Z
Answers.UserDisplayName: Lloyd_LiuSiyi
Body: <p>I want a list of all variants,  i.e. sites which are known to vary between human to human. For example, it should ideally cover all sites in <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working" rel="nofollow noreferrer">here</a>, but without samples.</p>
  <p>I don't want a giant reference panel with many samples, nor a .fa which has no major/minor allele information.</p>
  <p>I just want a file with the following information at each locus:</p>
  <ul>
  <li>Location (chromosome position and chromosome)</li>
  <li>Bonus (not necessary): rsID</li>
  <li>Major allele (i.e., A, C, T, or G) at that position</li>
  <li>Minor allele at that position</li>
  </ul>
  <p>I'm not picky about how major/minor alleles are defined. Usually they are defined as more common in the general population vs. less common (loosely). Conforming to b37 or b38 would be ideal.</p>
  <p>I'm looking for one such file that doesn't have samples in it, but does contain all possible positions (not all VCF files have this)</p>
  <p>Where can I download something like this? I like working with VCFs but any format is good.</p>
  
Tags: <vcf><data-download><rsid>
Title: Where to download a file with major and minor alleles at every position?
ThreadText: # Where to download a file with major and minor alleles at every position?
  
  (Asked by: username_0 on 2023-10-09)
  
  I want a list of all variants, i.e. sites which are known to vary between human to human. For example, it should ideally cover all sites in [here](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working), but without samples.
  
  I don't want a giant reference panel with many samples, nor a .fa which has no major/minor allele information.
  
  I just want a file with the following information at each locus:
  
  * Location (chromosome position and chromosome)
  * Bonus (not necessary): rsID
  * Major allele (i.e., A, C, T, or G) at that position
  * Minor allele at that position
  
  I'm not picky about how major/minor alleles are defined. Usually they are defined as more common in the general population vs. less common (loosely). Conforming to b37 or b38 would be ideal.
  
  I'm looking for one such file that doesn't have samples in it, but does contain all possible positions (not all VCF files have this)
  
  Where can I download something like this? I like working with VCFs but any format is good.
  
  **Tags:** vcf, data-download, rsid
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2023-10-10. Score: 3
  
  Sounds like you're looking for the [dbSNp](https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi) files. You haven't specified a species, but you can download the data for human from the [dbSNP FTP site](https://ftp.ncbi.nlm.nih.gov/snp/). Specifically, you want:
  
  ```
  wget https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
  
  ```
  
  This file has lines like:
  
  ```
  1   10848   rs1271898990    C   G   .   .   RS=1271898990;RSPOS=10848;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99998407237512742,0.00001592762487257
  1   10851   rs1340958514    G   A   .   .   RS=1340958514;RSPOS=10851;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99996018093781855,0.00003981906218144
  1   10854   rs1222740568    G   A,C .   .   RS=1222740568;RSPOS=10854;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99967348369011213,0.00019113149847094,0.00013538481141692
  1   10857   rs1487378566    C   G   .   .   RS=1487378566;RSPOS=10857;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000100;GENEINFO=DDX11L1:100287102;WGT=1;VC=SNV;R5;ASP;TOPMED=0.99933900356778797,0.00066099643221202
  
  ```
  
  However, it sounds like you might be underestimating the complexity here. There isn't just one minor allele, many sites have multiple minor alleles. The example above shows one such multiallelic site (you can split these into separate lines using `bcftools`). But you also have cases like:
  
  ```
  1   10786   rs1464509424    CGGCGCA C   .   .   RS=1464509424;RSPOS=10787;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP;TOPMED=0.99991239806320081,0.00008760193679918
  1   10786   rs1258377526    CGGCGCAGGCGCAGACACATGCTAGCGCGTCGGGGTGGAGGCGT    C   .   .   RS=1258377526;RSPOS=10787;dbSNPBuildID=151;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP
  
  ```
  
  Don't expect just one major and one minor allele per location.
  
  > **Comments:**
  > **username_0**: This is probably it, thanks. I looked on the dbSNP website but couldn't find the exact right file. I have a good method in place for handing multiallelic sites  
  
  ---
  
  ### Answer by username_2 on 2023-10-20. Score: 2
  
  I agree with @username_1 that perhaps dbSNP is what you may want to look at. The dbSNP155 RefSNP VCF file in GRCh37 version may help. It can be downloaded from <https://ftp.ncbi.nlm.nih.gov/snp/latest_release/vcf/GCF_000001405.25.gz>.
  
  You may also fine the 1000G genome website helpful. <https://www.internationalgenome.org/data-portal/data-collection> contains much of its release both in `.fa` format and in VCF format. I understand that a large number of samples included increase the file size tremendously, but it is necessary as you're not just looking at what the major and minor allele is, but also their frequency, which may vary greatly between populations. It's important to check which population we're seeing when using their genomic information.
  
  Hope my answer helps. Regards.
  
  
  ---
  
  