Command Overview
Binx provides a suite of commands for genomic analysis. Each command is designed to handle a specific task in the analysis pipeline.
Command Structure
All Binx commands follow the pattern:
binx <command> [options]
Get help for any command with --help:
binx --help # List all commands
binx gwas --help # Help for specific command
Available Commands
Analysis Commands
| Command | Description | Primary Use |
|---|---|---|
gwas | Genome-wide association study | Identify trait-associated markers |
kinship | Compute kinship matrix | Account for population structure |
dosage | Estimate genotype dosages | Process read count data |
Utility Commands
| Command | Description | Primary Use |
|---|---|---|
convert | Convert file formats | Prepare VCF data for analysis |
plot | Generate visualizations | Create Manhattan/QQ plots |
qtl | Extract QTLs | Identify significant loci |
threshold | Calculate thresholds | Determine significance cutoffs |
Typical Workflows
Basic GWAS Pipeline
# 1. Convert VCF to Binx format
binx convert --vcf data.vcf.gz --output geno.tsv --format gwaspoly
# 2. Compute kinship matrix
binx kinship --geno geno.tsv --ploidy 4 --out kinship.tsv
# 3. Run GWAS
binx gwas --geno geno.tsv --pheno pheno.csv --trait yield \
--kinship kinship.tsv --ploidy 4 --out results.csv
# 4. Visualize results
binx plot --input results.csv --output manhattan.svg --plot-type manhattan
With Dosage Estimation from VCF
# 1. Estimate dosages from VCF with allele depths
binx dosage --vcf data.vcf.gz --ploidy 4 --output geno.tsv --format gwaspoly
# 2. Continue with GWAS...
binx gwas --geno geno.tsv --pheno pheno.csv --out results.csv --trait yield --ploidy 4
Common Options
These options are available across multiple commands:
| Option | Description |
|---|---|
--help, -h | Display help information |
--version, -V | Display version information (top-level only) |
--verbose | Enable verbose output (where applicable) |
--threads | Number of threads (where applicable) |
--output or --out | Output file path (varies by command) |
Exit Codes
| Code | Meaning |
|---|---|
0 | Success |
1 | Error (invalid arguments, file not found, processing error, etc.) |
Next Steps
Explore individual command documentation:
- binx gwas - The main GWAS command
- binx kinship - Kinship matrix computation
- binx convert - File format conversion