This workflow can be used to call genotypes and SNPs following either our STACKS de novo workflow or reference-guided RAD analysis workflow.

The output of this workflow is a filtered VCF file containing genotype and SNP information for all samples in your dataset, and can be used for further filtering with the Radiatior R package, or generating population statistics.

The scripts_and_example_files folder in this repo contains all required scripts for this workflow and an example Radiator script.