Example datasets for testing the GWASTic software

The repository includes two datasets. The first dataset contains barley data to validate the peak associations of two-row barley genes previously identified in Milner, Jost, and Taketa (2019).

To replicate the Genome-Wide Association Study (GWAS) results, please use the pre-filtered and formatted genotypic file ‘WGS300_005_0020.bed’. The corresponding phenotype data for row type pre-formatted for direct use with the GWAStic software is available in ‘bridge_row_type_GWAS.txt’.

To reproduce the genomic prediction experiments, please use the same files:  ‘WGS300_005_0020.bed’ for the genotypic data and the ‘bridge_row_type_GP.txt’ for the phenotypes. The file ‘validation_set.txt’ contains a set of 30 genotypes that have been excluded from the training data for use as a validation set.

Additionally, a minimalistic dataset is provided to facilitate quick testing of the GWAStic software. This dataset includes:‘example.vcf.gz’ to test the VCF to BED conversion.‘example.bed’ is a filtered genotypic file ready for use.‘pheno_gwas.csv’ as a phenotypic file for GWAS.‘pheno_gp.csv’ as a phenotypic file for genomic prediction.