Dataset used to map a stump tail sperm defect of Swiss Large White boars

This dataset contains genotypes for 106 Swiss Large White boars that were used to map a stump tail sperm defect and a VCF file that contains genotypes of candiate variants for 87 boars.

The subdirectories contain plink binaries, corresponding phased haplotypes (in MaCH format), the results of a haplotype-based GWAS, and a VCF file that contains genotypes at candidate causal variants.

The affection status (case=2, control=1) of 106 boars is indicated in the file "pheno".

The R script "haplo_linear.R" performs the haplotype-based association study.

The README file provides instructions on how to run the GWAS as well as on how to create the Manhattan plot.