Great ape segregating sites

Segregating sites in the three great ape clades: <i>Pan</i>, <i>Gorilla</i>, <i>Pongo</i>.<i>Pan</i>: bonobos (<i>Pan paniscus</i>) and chimpanzees (<i>Pan troglodytes</i>, 4 subspecies)<i>Gorilla</i>: Eastern gorillas (<i>Gorilla beringei</i>, 2 subspecies) and Western gorillas (<i>Gorilla gorilla</i>, 2 subspecies)<i>Pongo</i>: Sumatran orangutan (<i>Pongo abelii</i>), Bornean orangutan (<i>Pongo pygmaeus</i>), Tapanuli orangutan (<i>Pongo tapanuliensis</i>).In total 141 individuals. Segregating sites within each clade for wild-born individuals with more than 12-fold genome-wide average coverage in VCF format. Raw data retrieved from European Nucleotide Archive (ENA), with identifiers from the original studies. Adapters removed with Trimmomatic 0.39, mapping with bwa mem 0.7.16a to the human reference genome version hg38 (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna), duplicates removed with gatk 4.1.4.0 MarkDuplicatesSpark, merging with samtools 1.14, genotype calling with gatk 4.1.4.0 HaplotypeCaller, merging with gatk 4.1.4.0 GenomicsDBImport and GenotypeGVCFs, concatenation with bcftools 1.19 concat.