Evaluating population structure in the northern bottlenose whale, Hyperoodon ampullatus, using genomic resequencing data

This dataset contains resequencing data used in our northern bottlenose whale genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection. Source code for genomic analyses is available at github.com/edegreef/NBW-resequencing. Data uploaded here contain:

• NBW_all_variantcalls.vcf.gz - All variant calls, including both indels and SNPs
• NBW_SNPS_unfiltered.vcf.gz - Unfiltered SNPs
• NBW_SNPS_filtered_population_analyses.vcf.gz - Filtered SNPs for population analyses. Filtered for quality (removed qual < 20, mq < 30, qd < 2, missingness > 0.4), non-biallelic sites, autosomes, structural variants, minor allele count 2, minimum scaffold length 50kb
• NBW_SNPS_filtered_pruned_population_analyses.vcf.gz - Additionally LD-pruned with r2 > 0.5
• NBW_SNPS_filtered_demography_analyses.vcf.gz - Filtered SNPs for demography analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, minimum scaffold length 100kb.
• NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, non-biallelic sites, autosomes, structural variants, max-missingness 0.1, minor allele count 2, minimum scaffold length 50kb.
• NBW_SNPS_filtered_Xchr.vcf.gz & NBW_SNPS_filtered_Ychr_males.vcf.gz - Filtered SNPs on X & Y chr. Filtered for quality, non-biallelic sites, structural variants, minor allele count 2, minimum scaffold length 50kb.