RAD-seq Variant Analysis

The radseq_variance_analysis.py script performs RAD-seq variant analysis to locate sequencing sites, detect variations within those sites, and calculate relevant statistics. It supports two modes: SingleRad and ddRad, which are different methods for sequencing based on restriction enzyme digestion.

Requirements

Before running the script, ensure you have the following dependencies installed:

• Python 3.x
• Required Python packages (install with conda/mamba):
  • pyvcf
  • pyfaidx
  • Bio.Restriction.Restriction_Dictionary

Example of running the script using example data:

• python radseq_variance_analysis.py Mzebra_GT3_Chr1.fasta YH_MC_samples_Chr1.vcf SingleRad EcoRI
• python radseq_variance_analysis.py Mzebra_GT3_Chr1.fasta YH_MC_samples_Chr1.vcf ddRad EcoRI --RE2 HindIII

Running the script

python radseq_analysis.py --GenomeFile /path/to/genome.fasta --Mode SingleRad --RE1 EcoRI --VCFFile /path/to/variants.vcf