Answers.Body: <p>The UCSC Genome Browser downloads page has old human genome assembly versions way back to the first human genome ever published (by UCSC in 2000).
  <a href="http://hgdownload.soe.ucsc.edu/downloads.html#human" rel="nofollow noreferrer">http://hgdownload.soe.ucsc.edu/downloads.html#human</a></p>
  
  <p>We also have a variety of archived dbSNP data up to dbSNP141 on hg38, dbSNP 131 on hg37, dbSNP126 on hg18:
  <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp141.txt.gz" rel="nofollow noreferrer">http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp141.txt.gz</a>
  <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz" rel="nofollow noreferrer">http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz</a>
  <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/snp126.txt.gz" rel="nofollow noreferrer">http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/snp126.txt.gz</a></p>
  
  <p>They're in a custom table format, which can be turned into VCF manually.</p>
  
  <p>You can also get all of this data from Table Browser and add filters, etc.:
  <a href="http://genome.ucsc.edu/cgi-bin/hgTables" rel="nofollow noreferrer">http://genome.ucsc.edu/cgi-bin/hgTables</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-01T00:23:46.150Z
Answers.LastActivityDate: 2020-02-01T00:23:46.150Z
Answers.UserDisplayName: dschmelt
Body: <p>For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP.</p>
  
  <p>Unfortunately it appears as though older versions of dbSNP aren’t archived, or at least these archives are not publicly accessible.</p>
  
  <p>In particular, <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/archive" rel="nofollow noreferrer">the NCBI FTP archive</a> is fairly sparse. The only pre-GRCh37 version it contains is ostensibly <a href="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=124" rel="nofollow noreferrer">dbSNP build 124 from January 2005</a>, for hg17 (NCBI build 35). Unfortunately <a href="ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/archive/human_9606_b124_NCBI35/" rel="nofollow noreferrer">the corresponding FTP folder is actually <em>empty</em></a>. dbSNP build 138 has been “removed to recover storage”, whatever that means, and I’m unclear which version of the human reference genome it refers to (its <a href="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=138" rel="nofollow noreferrer">official page</a> does not contain this rather crucial bit of information).</p>
  
  <p>Is there another authoritative source of this data?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-09T05:57:30.133Z
Comments.Text: Perhaps ENSEMBL will have some of what you need? At least the older reference genomes appear to be there. https://www.ensembl.org/info/data/ftp/index.html
Comments.UserDisplayName: Scot
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-09T08:28:35.710Z
Comments.Text: @Scot Ensembl has variation data but it does not, as far as I know, host the dbSNP data (i.e. a dataset exactly corresponding to a given dbSNP build). Although I might be able to filter the corresponding entries from their variant database, and convert it to VCF.
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-09T08:58:44.127Z
Comments.Text: Actually this won’t work: The NCBI36 variant data on Ensembl doesn’t contain dbSNP information directly, and it’s in a format that’s not trivial to convert to VCF.
Comments.UserDisplayName: Konrad Rudolph
Tags: <database><public-databases><variant-calling><reference-genome>
Title: Old versions of the reference genome and dbSNP
ThreadText: # Old versions of the reference genome and dbSNP
  
  (Asked by: username_0 on 2019-04-08)
  
  For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP.
  
  Unfortunately it appears as though older versions of dbSNP aren’t archived, or at least these archives are not publicly accessible.
  
  In particular, [the NCBI FTP archive](ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/archive) is fairly sparse. The only pre-GRCh37 version it contains is ostensibly [dbSNP build 124 from January 2005](https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=124), for hg17 (NCBI build 35). Unfortunately [the corresponding FTP folder is actually *empty*](ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/archive/human_9606_b124_NCBI35/). dbSNP build 138 has been “removed to recover storage”, whatever that means, and I’m unclear which version of the human reference genome it refers to (its [official page](https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?build_id=138) does not contain this rather crucial bit of information).
  
  Is there another authoritative source of this data?
  
  **Tags:** database, public-databases, variant-calling, reference-genome
  
  > **Comments:**
  > **username_1**: Perhaps ENSEMBL will have some of what you need? At least the older reference genomes appear to be there. https://www.ensembl.org/info/data/ftp/index.html  
  > **username_0**: @username_1 Ensembl has variation data but it does not, as far as I know, host the dbSNP data (i.e. a dataset exactly corresponding to a given dbSNP build). Although I might be able to filter the corresponding entries from their variant database, and convert it to VCF.  
  > **username_0**: Actually this won’t work: The NCBI36 variant data on Ensembl doesn’t contain dbSNP information directly, and it’s in a format that’s not trivial to convert to VCF.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-02-01. Score: 2
  
  The UCSC Genome Browser downloads page has old human genome assembly versions way back to the first human genome ever published (by UCSC in 2000).
  <http://hgdownload.soe.ucsc.edu/downloads.html#human>
  
  We also have a variety of archived dbSNP data up to dbSNP141 on hg38, dbSNP 131 on hg37, dbSNP126 on hg18:
  <http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp141.txt.gz>
  <http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp138.txt.gz>
  <http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/snp126.txt.gz>
  
  They're in a custom table format, which can be turned into VCF manually.
  
  You can also get all of this data from Table Browser and add filters, etc.:
  <http://genome.ucsc.edu/cgi-bin/hgTables>
  
  
  ---
  
  