Resources for genomic analyses in baboons (genus Papio)

Resources for genomic analyses in baboons (genus Papio). See "Analysis of 100 high coverage genomes from a pedigreed captive baboon colony" by Robinson et al. 2019 for further details.

Panu_2.0_Panu_3.0_chain_files.tar.gz 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).

baboon_100_highcoverage_SNPRC_sample_info.txt 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.

baboon_24_olive_founders_phased.vcf.gz 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. baboon_24_olive_founders_phased.vcf.gz.tbi is the index for the VCF file.

baboon_ldhelmet_recombination_maps.tar.gz 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).

baboon_AIMs_33founders_fixed_yellow_olive.txt 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.

baboon_plink_ROH.bed 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.

baboon_LOF_mutations.txt 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”.