binx qtl

Identify and filter significant QTLs from GWAS results.

Synopsis

binx qtl [OPTIONS]

The qtl command processes GWAS results to identify significant quantitative trait loci (QTLs). It filters markers where score >= threshold and optionally prunes nearby signals within a specified window.

Important: The input file must contain a threshold column. Use binx gwas --threshold to generate results with thresholds, or binx threshold to calculate thresholds separately.

Tip: If your results file doesn’t have a threshold column, see Adding Thresholds to Existing Results for instructions on how to add one.

Options

Option	Default	Description
`--input <FILE>`	stdin	Input GWAS results file
`--output <FILE>`	stdout	Output file path
`--bp-window <INT>`	-	Prune signals within this window (bp)

Examples

Basic QTL Extraction

binx qtl \
  --input gwas_results.csv \
  --output qtls.csv

With Window-based Pruning

Prune nearby signals within a 1 Mb window:

binx qtl \
  --input gwas_results.csv \
  --bp-window 1000000 \
  --output qtls.csv

Pipeline from GWAS

Pipe directly from GWAS with threshold calculation:

binx gwas \
  --geno geno.tsv \
  --pheno pheno.csv \
  --trait yield \
  --ploidy 4 \
  --threshold m.eff \
  --out /dev/stdout 2>/dev/null | \
binx qtl --bp-window 1000000 --output qtls.csv

Reading from stdin

cat gwas_results.csv | binx qtl --bp-window 1000000

Output Format

Column	Description
`marker_id`	Peak marker identifier
`chrom`	Chromosome
`pos`	Base pair position
`model`	Genetic model used
`score`	-log10(p-value)
`effect`	Effect size estimate
`threshold`	Significance threshold used

Example Output

marker_id,chrom,pos,model,score,effect,threshold
SNP_1_1500,1,1500,additive,7.92,0.82,5.0
SNP_3_8200,3,8200,additive,5.51,0.45,5.0

Algorithm

The QTL detection algorithm (matching R/GWASpoly’s get.QTL):

Filter significant markers: Keep only markers where score >= threshold
Group by model: Process each genetic model separately
Sort by significance: Order markers by score (descending)
Window-based pruning (if --bp-window specified):
- For each chromosome, iterate through markers from most to least significant
- Keep a marker only if it’s more than bp-window away from all previously retained markers
- This ensures the most significant marker in each region is retained

Binx Documentation