This repository contains the main workflows generated for assessing the impact of the reference assembly choice on bovine genomic analyses. The repository is split into two main sections:

1. Alignment pipeline and mapping statistics

• Snakemake workflow developed for aligning raw data (FASTQ files) to a reference genome.
• Main mapping statistics extracted out of the aligned files (BAM).

2. Sequence variant genotyping, variant calling and imputation

• Snakemake and bash workflows developed for variant genotyping. Separate pipelines are developed for the following processes:

  • Haplotype caller
  • Joing genotyping
  • Variant filtration and imputation

Developed for analysis of bovine genomes, should be applicable to the other species as well.

Did you use the pipeline/scripts for your research? Please, cite as indicated below:

Lloret-Villas, et. al. Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. Biorxiv