Scripts and commands used for Hawaiian Metrosideros polymorpha project by Choi et al.

Start from FASTQ to end with with VCF

Use commands outlined in Choi et al. 2019 Plos Genet study

https://github.com/cjy8709/Choi_etal_O.glaberrima_PopGenome/blob/master/FromFASTQ_to_VCF.sh

ANGSD analysis

Slurm scripts associated with ANGSD analysis

ANGSD/ANGSD_commands.txt

Analysis involving examining the population relationships

Commands and scripts used for Treemix, f4 test, and Twisst analysis

POPULATION_RELATIONSHIP/POPULATION_RELATIONSHIP_commands.txt

Sweep analysis

Commands and scripts used for Omegaplus, H12, and Hscan statsitics calculation

SWEEPS/SWEEP_commands.txt