Genotype data for 91 Braunvieh and 161 Fleckvieh individuals

Context and methodology 

This dataset was created as part of a research project focusing on investigating recombination rates and genomic features for two Swiss cattle breeds and it offers genotypic data for 91 Braunvieh and 161 Fleckvieh individuals, specifically focusing on chromosome 25. 

Through this dataset, researchers gain insight into genetic variations, including single nucleotide polymorphism (SNPs) and insertions and deletions (INDELs), enabling deeper investigations into breed-specific characteristics.

The genotypic data was generated via high-throughput sequencing and genotyping techniques, involving blood sample collection, DNA extraction, and sequencing using Illumina HiSeq X platform. Analysis pipelines, starting with data preprocessing and alignment, followed by variant calling and quality filtering, were employed. The resulting VCF files contain detailed genotype information, serving as a foundation for population genetics studies. These genotype data serve as the foundation for downstream analyses, including the estimation of recombination rates and the investigation of genomic features such as SNP density and GC content in the respective cattle breeds.

Technical details 

The dataset consists of four VCF files, each representing genotypic information for a specific subset of individuals within the Braunvieh and Fleckvieh cattle breeds. The VCF files are named according to the breed (Braunvieh or Fleckvieh) and the part number, along with the date of creation (e.g., braunvieh_part1_20072019.vcf). Furthermore, there is a README file describing the VCF files. 

The VCF files can be opened and viewed using standard text editors, such as Notepad on Windows or TextEdit on macOS. This allows researchers to inspect the contents of the files and understand the structure of the genetic variant data. 

For more advanced analysis and manipulation of the genotype data, researchers may require bioinformatics software capable of handling VCF files, such as Genome Analysis Toolkit (GATK), SAMtools, or Variant Call Format (VCF) tools. 

Additionally, software for statistical analysis and visualization, such as R or Python with relevant libraries, may be needed for downstream analysis of the genotype data. 

Further details 

Please note that the dataset is restricted, and access must be requested for data reuse.