These scripts can be used to auto-generate and call pbs scripts on Georgia Tech's PACE server. While these scripts are used in the Streelman lab on cichlid genomes, the scripts are flexible enough to work with any genome.
Follow the workflow described in the README of the Variant Calling folder to produce a vcf file. Then use the scripts in the Fst folder to calculate the calculate and visual fst scores from the vcf file.
Variant Calling: This folder contains scripts used for variant calling, which is used to identify variants (i.e. single-nucleotide-polymorphisms, indels, and structural differences) from the reference sequence.
Fst: This folder contains scripts to calculate and visual Fst scores, which can be helpful in determing genetic differences in populations.