Dataset Open Access
Jacqueline A. Robinson;
Saurabh Belsare;
Shifra Birnbaum;
Deborah E. Newman;
Jeannie Chan;
Jeremy P. Glenn;
Betsy Ferguson;
Laura A. Cox;
Jeffrey D. Wall
<?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"><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> <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> <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> <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> <p><br> <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> <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> <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> <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></description> </descriptions> </resource>
All versions | This version | |
---|---|---|
Views | 366 | 366 |
Downloads | 168 | 168 |
Data volume | 8.6 GB | 8.6 GB |
Unique views | 315 | 315 |
Unique downloads | 89 | 89 |