The Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) 5.0 genotyping-by-sequencing (GBS) standalone pipeline version 2.0 produces a variant calling format (VCF) file which is always coded a major/minor allele, regardless of passed options. This program, written in Bash, is made to fix this and recode the alleles in reference/alternative. The program has three dependencies: vcftools, bcftools and bedtools.
These combined tools are used to reference an indexed reference sequence file (.fa) and identify which single nucleotide polymorphisms (SNPs) in a VCF are coded properly in reference/alternate format and which must be changed to refelect a true reference/alternate. For help on running the program, refer to the usage function by running the shell script (.sh) with the help option (-h,-help).