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Genotype data¤

jaxQTL uses genoio for genotype input/output.

Choose an input format¤

Each mapping command requires exactly one of the following source options. For PLINK inputs, pass the shared filename prefix; for VCF/BCF and BGEN, pass the file path.

Source option Required input With --dosage
--bfile PREFIX PLINK1: .bed, .bim, and .fam Unsupported; hard calls only
--pfile PREFIX PLINK2: .pgen, .pvar (or .pvar.zst), and .psam Reads stored biallelic dosages
--vcf PATH Indexed VCF or BCF Reads FORMAT/DS instead of FORMAT/GT
--bgen PATH BGEN Required; reads expected allele counts from probabilities

BGEN support covers v1.2+ Layout 2 biallelic diploid records. Sample IDs must be embedded in the BGEN file or provided in a same-prefix .sample file so they can be aligned with phenotype and covariate IDs.

Choose hard calls or dosages¤

--dosage is a separate flag used alongside a source option, for example --vcf cohort.vcf.gz --dosage or --bgen cohort.bgen --dosage. It takes no value and does not select a file format.

Without it, jaxQTL requests hard-call allele counts (0, 1, or 2 for diploid genotypes). Dosages are expected allele counts and can be fractional, preserving uncertainty in imputed genotypes. The reader does not convert dosages into hard calls; VCF dosage reads require DS, rather than deriving values from GP.

To use imputed VCF dosages in the Quickstart, replace its --bfile tutorial/input/chr22_N100 argument with --vcf cohort.vcf.gz --dosage and supply matching phenotype and covariate files.

The counted allele is a1

jaxQTL preserves the genoio allele convention: genotype values count a1. Output effect estimates therefore describe a one-unit increase in the a1 count or dosage.

Filter and match inputs¤

Use --maf FLOAT to exclude variants below a minimum minor-allele frequency. The filter is applied by the genotype reader before cis regions or trans blocks are converted to JAX arrays.

By default, mapping retains expression phenotypes only on exact chromosome labels present in the genotype input. Use --chr LABEL to restrict both expression phenotypes and genotype variants to one chromosome. Labels are matched exactly: for example, chr22 and 22 are different labels. The requested label must occur in both inputs.

Variant metadata must provide chromosome, position, identifier, and a0/a1 alleles through the selected genoio adapter. jaxQTL computes allele frequency and minor-allele count from the loaded genotype values.