binx convert

Convert VCF files to Binx-compatible formats.

Synopsis

binx convert --vcf <FILE> --output <FILE> [OPTIONS]

Description

The convert command transforms VCF (Variant Call Format) files into tabular formats used by Binx. It provides two output formats:

• csv: Extracts allele depths (AD field) as two-line ref/total counts for use with binx dosage
• gwaspoly: Extracts genotype dosages (from GT field) for direct use with binx gwas

Required Arguments

Options

Output Formats

csv (default)

Outputs allele depths in a two-line format suitable for binx dosage:

• Reads the AD (Allelic Depths) field from the VCF
• First line for each locus: reference allele counts
• Second line for each locus: total read counts

locus,Sample1,Sample2,Sample3
SNP001,10,2,15
SNP001,15,20,18
SNP002,8,12,5
SNP002,16,25,10

Use this format when you want to estimate dosages with binx dosage.

gwaspoly

Outputs genotype dosages in GWASpoly format suitable for binx gwas:

• Reads the GT (Genotype) field from the VCF
• Converts genotypes to dosage values (count of alternate alleles)
• Handles missing genotypes as NA

Marker	Chrom	Position	Sample1	Sample2	Sample3
SNP001	chr1	1000	0	2	4
SNP002	chr1	2000	1	1	3

Use this format when your VCF has reliable genotype calls.

Examples

Convert VCF to Allele Depths (for dosage estimation)

binx convert \
  --vcf variants.vcf.gz \
  --format csv \
  --output allele_depths.csv

Then estimate dosages:

binx dosage \
  --csv allele_depths.csv \
  --ploidy 4 \
  --output genotypes.tsv

Convert VCF to GWASpoly Format (direct use)

binx convert \
  --vcf variants.vcf.gz \
  --format gwaspoly \
  --output genotypes.tsv

Then run GWAS directly:

binx gwas \
  --geno genotypes.tsv \
  --pheno phenotypes.csv \
  --trait yield \
  --ploidy 4 \
  --out results.csv

With Verbose Output

binx convert \
  --vcf variants.vcf.gz \
  --format gwaspoly \
  --output genotypes.tsv \
  --verbose

VCF Requirements

For csv format (allele depths)

The VCF must contain the AD (Allelic Depths) field in the FORMAT column:

#CHROM  POS     ID      REF  ALT  QUAL  FILTER  INFO  FORMAT        Sample1       Sample2
chr1    1000    SNP001  A    T    .     .       .     GT:AD:DP      0/1:10,5:15   1/1:2,18:20

For gwaspoly format (genotype dosages)

The VCF must contain the GT (Genotype) field:

#CHROM  POS     ID      REF  ALT  QUAL  FILTER  INFO  FORMAT  Sample1     Sample2
chr1    1000    SNP001  A    T    .     .       .     GT      0/0/0/1     0/0/1/1

Polyploid genotypes are supported (e.g., 0/0/0/1 for tetraploid).

Choosing Between Formats

See Also

• binx dosage - Estimate dosages from allele depths
• binx gwas - Run GWAS with genotype data
• Input Formats