VCF files for "Pan-genome Analysis Reveals Hidden Diversity and Selection Signatures of Auxin Response Factors (ARFs) Associated with Breeding in Barley"

This dataset contains SNP and INDEL variant calls for 76 barley genotypes, generated by re-mapping 76 pan-genome assemblies to the Morex V2 reference genome. For details please check method part of publication. The main output is a multi-sample VCF file (merged_all.vcf.gz) containing the variant calls across all genotypes. An associated index file (merged_all.vcf.gz.csi) is also provided to enable fast querying. To facilitate downstream analysis and region-specific SNP extraction, a simple bash script get_vcf.bash is included. Also provided is an example file morex_v2_arf_location.txt, which can be used as an input for region-based extraction (e.g., for use with get_matrix.bash).