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


DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="DOI">10.5281/zenodo.2583292</identifier>
  <creators>
    <creator>
      <creatorName>Jacqueline A. Robinson</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-5556-815X</nameIdentifier>
      <affiliation>University of California, San Francisco</affiliation>
    </creator>
    <creator>
      <creatorName>Saurabh Belsare</creatorName>
      <affiliation>University of California, San Francisco</affiliation>
    </creator>
    <creator>
      <creatorName>Shifra Birnbaum</creatorName>
      <affiliation>Texas Biomedical Research Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Deborah E. Newman</creatorName>
      <affiliation>Texas Biomedical Research Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Jeannie Chan</creatorName>
      <affiliation>Texas Biomedical Research Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Jeremy P. Glenn</creatorName>
      <affiliation>Texas Biomedical Research Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Betsy Ferguson</creatorName>
      <affiliation>Oregon National Primate Research Center</affiliation>
    </creator>
    <creator>
      <creatorName>Laura A. Cox</creatorName>
      <affiliation>Wake Forest School of Medicine</affiliation>
    </creator>
    <creator>
      <creatorName>Jeffrey D. Wall</creatorName>
      <affiliation>University of California, San Francisco</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Resources for genomic analyses in baboons (genus Papio)</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <dates>
    <date dateType="Issued">2019-03-01</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/2583292</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2583291</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode">Creative Commons Attribution Non Commercial No Derivatives 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Resources for genomic analyses in baboons (genus &lt;em&gt;Papio&lt;/em&gt;). See &amp;quot;Analysis of 100 high coverage genomes from a pedigreed captive baboon colony&amp;quot; by Robinson et al. 2019 for further details.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Panu_2.0_Panu_3.0_chain_files.tar.gz&lt;/strong&gt; 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).&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;baboon_100_highcoverage_SNPRC_sample_info.txt&lt;/strong&gt; 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.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;baboon_24_olive_founders_phased.vcf.gz&lt;/strong&gt; 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. &lt;strong&gt;baboon_24_olive_founders_phased.vcf.gz.tbi&lt;/strong&gt; is the index for the VCF file.&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
&lt;strong&gt;baboon_ldhelmet_recombination_maps.tar.gz&lt;/strong&gt; 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).&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;baboon_AIMs_33founders_fixed_yellow_olive.txt&lt;/strong&gt; 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.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;baboon_plink_ROH.bed&lt;/strong&gt; 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.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;baboon_LOF_mutations.txt&lt;/strong&gt; List of putative LOF mutations annotated with SnpEff (Cingolani et al. 2012, DOI:10.4161/fly.19695). The following mutation types were included: &amp;ldquo;stop_gained&amp;rdquo;, &amp;ldquo;start_lost&amp;rdquo;, &amp;ldquo;stop_lost&amp;rdquo;, &amp;ldquo;splice_acceptor_variant&amp;rdquo;, &amp;ldquo;splice_donor_variant&amp;rdquo;.&lt;/p&gt;</description>
  </descriptions>
</resource>
190
102
views
downloads
All versions This version
Views 190190
Downloads 102102
Data volume 4.4 GB4.4 GB
Unique views 167167
Unique downloads 4141

Share

Cite as