Usage

Command-Line Arguments

• --vcf: Path to the input VCF file (compressed with gzip, .vcf.gz).
• --genotype_field: Genotype field to analyze (GT, PGT, or both). Default is GT.
• --chromosome: (Optional) Chromosome to filter (e.g., chr1).
• --start_bp: (Optional) Start base pair position for filtering.
• --end_bp: (Optional) End base pair position for filtering.
• --phenotype: Path to the phenotype file (tab-delimited text file).
• --sample_id_col: Column name for sample IDs in the phenotype file.
• --phenotype_col: Column name for the binary phenotype in the phenotype file.
• --covariate_cols: (Optional) Column names for covariates in the phenotype file (space-separated).
• --method: Association test method (fisher or logistic). Default is fisher.
• --output: Output file name for the results (e.g., results.txt).

Example Command

python association_test.py \
    --vcf input.vcf.gz \
    --genotype_field GT \
    --phenotype phenotype.txt \
    --sample_id_col SampleID \
    --phenotype_col CaseControl \
    --covariate_cols Age Sex \
    --method fisher \
    --output results.txt