Calculating Pairwise FST

  1. Obtain scripts: SAF.sh & pwfst.sh

  2. Create a bamlist with individuals from only the “population” you want to test

  3. Generate a simple allele frequencies file (.saf) for every “population” bamlist you want to compare, requires bamlist, outfile name, and your ancestral/alignment file (i.e., ___300.fasta)

    • sbatch -t 24:00:00 - p high SAF.sh bamlist outfile_name ancestral_file

  4. For pairwise comparisons between “populations”, use two ____.saf.index files you just generated:

    • sbatch -t 24:00:00 -p high pwfst.sh pop1 pop2 where pop1 is the filename (no extension) of the 1st ___.saf.index and pop2 is the 2nd
    • find the output files: ls *finalfstout to view. The adjusted FST is the second value.