statMix

The statMix package is intended to be used to reduce compuational knowledge and time for population genetic analyses. It uses several elements from the PPP pipeline (Webb et al., 2021) and VCFtools (Danecek et al., 2011). The idea is that all the user has to do is provide a vcf file, select which analyses they would like to perform, and hit play -- the software will do everything else.

How to use

Install statMix

1. Clone this repo onto your machine: git clone https://github.com/raywray/statMix.git
2. Install all necessary conda packages and create a conda environment (will need to have anaconda or minicoda installed prior) with the following command: conda env create -f environment.yml
3. Activate the conda environment: conda activate stat_mix_env

Use statMix

All statMix needs is a vcf file of your population(s) and your choice of summary statistics to run.

• hwe: Calculates Hardy Weinberg Equilibrium
• pop_structure: Runs a full population structure analysis using admixture and creates plots
• sfs: Generates SFS based on the population structure results
• generic_stats: Calculates all 'generic' stats:
  • tajima's D
  • windowed weir Fst
  • weir Fst
  • site pi
  • site pi per population (from population structure analysis)
  • windowed pi
  • windowed pi per population (from population structure analysis)
  • Fit
  • Fis
  • allele frequency
• fsc: Generates SFS compatible for fastsimcoal analyses
• pixy: Calculates statistics (pi, Fst, dxy) using pixy
• ima: Runs an IMa3 analysis (NOTE: unfinished)
• f_stats: Calculates Eigenstrat F statistics (NOTE: unfinished)

(NOTE: in order to run sfs, generic_stats, fsc, ima or pixy, you MUST have pop_structure too). See python3 statmix.py --help for more information.

Example Usage

python3 statmix.py --vcf tigers.vcf --out-prefix tigers --analyses hwe pop_structure sfs generic_stats fsc

Output

All results/visualizations can be found in respective subfolders of the output directory