Big cat vcf files from: Exceedingly low genetic diversity in snow leopards due to persistently small population size

Snow leopards (Panthera uncia) serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous Anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. In particular, the dearth of genetic data, unique among all big cat species, hinders a full understanding of their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer new insights into these unresolved aspects of snow leopard biology. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin–as previously identified using landscape models and fecal microsatellite markers–and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest g..., Calling SNPs in all big cat species:
We included all other species in the genus Panthera (leopard, lion, tiger, jaguar) as well as cheetah and puma. Accession numbers of publicly available WGS data and reference genomes used in this analysis are listed in Supplementary Table 3 and 4, respectively. We mapped all FASTQ data to the corresponding reference genome using BWA-MEM. We sorted and indexed resulting bam files using SAMtools. We added read groups and marked duplicates using picard. We calculated depth of coverage and breadth of coverage for each sample using SAMtools. We then used GATK HaplotypeCaller to generate a GVCF file for each sample and GATK CombineGVCFs to combine the GVCF files for every species (or subgroup in the case of tigers and leopards). Lastly, we used GATK GenotypeGVCFs to create a final VCF file for every group.
In order to limit the need for excessive computing power, we downsampled some samples with over 30X coverage using SAMtools view as indicated in Su..., # Big cat vcf files from: Exceedingly low genetic diversity in snow leopards due to persistently small population size

Dataset DOI: [10.5061/dryad.1vhhmgr78](https://doi.org/10.5061/dryad.1vhhmgr78)

## Description of the data and file structure

SNPs were called in our focal species, snow leopards (*Panthera uncia*), as well as all other big cat species using publicly available data. SNPs were called using the same pipeline in all species in order to make comparisons among the species. What we share here are the final filtered vcf files used in our analyses

Additionally, in snow leopards, SNPs were also called by a service provider, Gencove Inc., so there are two vcf files for snow leopards. 

Sample data for snow leopard vcfs can be found in Supplementary Table 1. 

Sample data for other big cat vcfs can be found in Supplementary Table 3. 

Details regarding which reference genomes were used for each vcf can be found in Supplementary Table 4.

### Files and variables

#### File: Pum...,