binx kinship

Compute kinship (genomic relationship) matrices from genotype data.

Synopsis

binx kinship --geno <FILE> --ploidy <INT> --out <FILE> [OPTIONS]

The kinship command computes a genomic relationship matrix (GRM) from marker dosage data. The kinship matrix captures genetic similarity between individuals and is used in GWAS to account for population structure and relatedness.

When to use: While binx gwas auto-generates a kinship matrix if not provided (using gwaspoly-rs’s set_k()), pre-computing with binx kinship is recommended when:

Running GWAS on multiple traits (avoids recomputation)

You need a specific kinship method (VanRaden vs GWASpoly)

You want to inspect or reuse the kinship matrix

Required Arguments

Argument	Description
`--geno <FILE>`	Path to genotype file (TSV/CSV with dosages)
`--ploidy <INT>`	Ploidy level (e.g., 2, 4, 6)
`--out <FILE>`	Output file path

Options

Option	Default	Description
`--method <METHOD>`	vanraden	Kinship method: `vanraden` or `gwaspoly`

Methods

VanRaden (default)

The standard VanRaden (2008) Method 1 additive relationship matrix, extended for polyploids:

K = M'M / (ploidy × Σ pq)

Where:

M is the centered genotype matrix (markers × samples)
Centering: dosage - (ploidy × p)
p = allele frequency, q = 1-p

GWASpoly

GWASpoly-style kinship matching R/GWASpoly’s set.K() function:

K = MM' / mean(diag(K))

Where M is centered by column means and normalized to have unit diagonal mean.

Examples

Basic Usage (Tetraploid)

binx kinship \
  --geno genotypes.tsv \
  --ploidy 4 \
  --out kinship.tsv

Using GWASpoly Method

binx kinship \
  --geno genotypes.tsv \
  --ploidy 4 \
  --method gwaspoly \
  --out kinship.tsv

For Diploids

binx kinship \
  --geno genotypes.tsv \
  --ploidy 2 \
  --out kinship.tsv

Output Format

A symmetric matrix with sample IDs as row and column headers:

sample_id	Sample1	Sample2	Sample3
Sample1	1.0000	0.2534	0.1256
Sample2	0.2534	1.0000	0.1892
Sample3	0.1256	0.1892	1.0000

Tips

Pre-compute for multiple traits: Compute kinship once and reuse across multiple GWAS runs
Check diagonal values: Diagonal values should be close to 1.0; much higher values may indicate inbreeding or data issues
Method selection: Use vanraden (default) for standard GWAS, or gwaspoly for compatibility with R/GWASpoly workflows

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