Dataset Open Access

Resources for genomic analyses in baboons (genus Papio)

Jacqueline A. Robinson; Saurabh Belsare; Shifra Birnbaum; Deborah E. Newman; Jeannie Chan; Jeremy P. Glenn; Betsy Ferguson; Laura A. Cox; Jeffrey D. Wall


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{
  "description": "<p>Resources for genomic analyses in baboons (genus <em>Papio</em>). See &quot;Analysis of 100 high coverage genomes from a pedigreed captive baboon colony&quot; by Robinson et al. 2019 for further details.</p>\n\n<p><strong>Panu_2.0_Panu_3.0_chain_files.tar.gz</strong> Chain files for converting coordinates between Panu_2.0 and Panu_3.0. All coordinates in the files below correspond to Panu_2.0, but can be converted to coordinates in the new assembly, Panu_3.0, using the chain files with liftOver (Hinrichs et al. 2006, DOI:10.1093/nar/gkj144).</p>\n\n<p><strong>baboon_100_highcoverage_SNPRC_sample_info.txt</strong> Sample information: Sample ID, Sequencing ID, Type, Sex, Fped (%), Admixed, Mean coverage (X). The type, sex, inbreeding coefficient (Fped), and admixture status are all based on the SNPRC pedigree.</p>\n\n<p><strong>baboon_24_olive_founders_phased.vcf.gz</strong> Phased VCF files for 24 olive baboon founders. Phasing was performed with Beagle (Browning and Browning 2007, DOI:10.1086/521987), assuming an effective population size of 40,000 individuals (Boissinot et al. 2014, DOI:10.1002/ajpa.22618). SNPs were filtered to remove singletons and thinned so that no two sites were closer than 10 bp. <strong>baboon_24_olive_founders_phased.vcf.gz.tbi</strong> is the index for the VCF file.</p>\n\n<p><br>\n<strong>baboon_ldhelmet_recombination_maps.tar.gz</strong> Fine-scale recombination maps produced with LDhelmet (Chan et al. 2012, DOI:10.1371/journal.pgen.1003090) based on phased genotypes from 24 olive baboon founders. Results from three block penalties are provided (5, 25, 50).</p>\n\n<p><strong>baboon_AIMs_33founders_fixed_yellow_olive.txt</strong> List of ancestry informative markers for distinguishing olive and yellow baboon ancestry. These sites represent fixed differences between 7 genetically yellow and 24 genetically olive baboons.</p>\n\n<p><strong>baboon_plink_ROH.bed</strong> Coordinates of runs of homozygosity in BED format, inferred with PLINK (Chang et al. 2015, DOI:10.1186/s13742-015-0047-8) using the default behavior of the --homozyg function. The following parameters were used to prune SNPs beforehand: --indep-pairwise 50 5 0.5. The columns are: chromosome, start position, end position, sample name.</p>\n\n<p><strong>baboon_LOF_mutations.txt</strong> List of putative LOF mutations annotated with SnpEff (Cingolani et al. 2012, DOI:10.4161/fly.19695). The following mutation types were included: &ldquo;stop_gained&rdquo;, &ldquo;start_lost&rdquo;, &ldquo;stop_lost&rdquo;, &ldquo;splice_acceptor_variant&rdquo;, &ldquo;splice_donor_variant&rdquo;.</p>", 
  "license": "https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "University of California, San Francisco", 
      "@id": "https://orcid.org/0000-0002-5556-815X", 
      "@type": "Person", 
      "name": "Jacqueline A. Robinson"
    }, 
    {
      "affiliation": "University of California, San Francisco", 
      "@type": "Person", 
      "name": "Saurabh Belsare"
    }, 
    {
      "affiliation": "Texas Biomedical Research Institute", 
      "@type": "Person", 
      "name": "Shifra Birnbaum"
    }, 
    {
      "affiliation": "Texas Biomedical Research Institute", 
      "@type": "Person", 
      "name": "Deborah E. Newman"
    }, 
    {
      "affiliation": "Texas Biomedical Research Institute", 
      "@type": "Person", 
      "name": "Jeannie Chan"
    }, 
    {
      "affiliation": "Texas Biomedical Research Institute", 
      "@type": "Person", 
      "name": "Jeremy P. Glenn"
    }, 
    {
      "affiliation": "Oregon National Primate Research Center", 
      "@type": "Person", 
      "name": "Betsy Ferguson"
    }, 
    {
      "affiliation": "Wake Forest School of Medicine", 
      "@type": "Person", 
      "name": "Laura A. Cox"
    }, 
    {
      "affiliation": "University of California, San Francisco", 
      "@type": "Person", 
      "name": "Jeffrey D. Wall"
    }
  ], 
  "url": "https://zenodo.org/record/2583292", 
  "datePublished": "2019-03-01", 
  "@context": "https://schema.org/", 
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      "contentUrl": "https://zenodo.org/api/files/330eb795-1590-47a0-ab54-f5c168c7e584/baboon_100_highcoverage_SNPRC_sample_info.txt", 
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      "contentUrl": "https://zenodo.org/api/files/330eb795-1590-47a0-ab54-f5c168c7e584/baboon_24_olive_founders_phased.vcf.gz", 
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      "contentUrl": "https://zenodo.org/api/files/330eb795-1590-47a0-ab54-f5c168c7e584/baboon_ldhelmet_recombination_maps.tar.gz", 
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      "contentUrl": "https://zenodo.org/api/files/330eb795-1590-47a0-ab54-f5c168c7e584/baboon_LOF_mutations.txt", 
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    {
      "contentUrl": "https://zenodo.org/api/files/330eb795-1590-47a0-ab54-f5c168c7e584/baboon_plink_ROH.bed", 
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    {
      "contentUrl": "https://zenodo.org/api/files/330eb795-1590-47a0-ab54-f5c168c7e584/Panu_2.0_Panu_3.0_chain_files.tar.gz", 
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  "identifier": "https://doi.org/10.5281/zenodo.2583292", 
  "@id": "https://doi.org/10.5281/zenodo.2583292", 
  "@type": "Dataset", 
  "name": "Resources for genomic analyses in baboons (genus Papio)"
}
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