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
{ "publisher": "Zenodo", "DOI": "10.5281/zenodo.2583292", "author": [ { "family": "Jacqueline A. Robinson" }, { "family": "Saurabh Belsare" }, { "family": "Shifra Birnbaum" }, { "family": "Deborah E. Newman" }, { "family": "Jeannie Chan" }, { "family": "Jeremy P. Glenn" }, { "family": "Betsy Ferguson" }, { "family": "Laura A. Cox" }, { "family": "Jeffrey D. Wall" } ], "issued": { "date-parts": [ [ 2019, 3, 1 ] ] }, "abstract": "<p>Resources for genomic analyses in baboons (genus <em>Papio</em>). See "Analysis of 100 high coverage genomes from a pedigreed captive baboon colony" 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: “stop_gained”, “start_lost”, “stop_lost”, “splice_acceptor_variant”, “splice_donor_variant”.</p>", "title": "Resources for genomic analyses in baboons (genus Papio)", "type": "dataset", "id": "2583292" }
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