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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    <dct:title>Resources for genomic analyses in baboons (genus Papio)</dct:title>
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    <dct:description>&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;</dct:description>
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