genoABO

genoABO infers genetically determined ABO blood group from VCF, BGEN, PGEN, and PLINK genotype datasets.

pip install genoabo
genoabo biobank.pgen --out bloodgroup

Research use only. genoABO is intended for population-genetics, epidemiology, GWAS, PheWAS, and biobank research. Genotype-inferred ABO groups do not capture all rare, weak, cis-AB, structural, or otherwise atypical ABO alleles and must not be used for transfusion or clinical decision-making.

Quick start

genoabo cohort.pgen --out abo
# writes: abo.abo.tsv, abo.qc.tsv, abo.summary.txt, abo.report.html

See docs/usage.md for the full CLI and Python API.

See docs/workflow.md for the full load-to-output pipeline.

See examples/ for VCF (unphased and phased), PGEN, and PLINK1 demos across builds and marker notations, a 1000 Genomes EAS four-marker example (phased --phase auto, or forced unphased), a multi-ancestry --assume-bo check against phased 1KG AFR/AMR/EAS/EUR, and marker LD r².

Inspect markers without calling:

genoabo cohort.pgen --inspect

Supported formats

Methods

genoabo --methods
genoabo --method-info three-marker
genoabo data.pgen --method auto        # default
genoabo data.pgen --method common
genoabo data.pgen --method three-marker
genoabo data.pgen --method ukb
genoabo data.pgen --method extended

Options

--format auto|vcf|bcf|bgen|pgen|plink1
--build auto|hg19|hg38|chm13
--geno-mode auto|hardcall|dosage|probability
--phase auto|phased|unphased
--assume-bo / --no-assume-bo
--min-genotype-prob 0.90
--dosage-hardcall-threshold 0.1
--strict-method
--inspect
--report PATH.html

Full option list: docs/usage.md.

Python API

from genoabo import ABOCaller

caller = ABOCaller(method="auto", build="auto")
result = caller.call("ukb.pgen")
for call in result.calls:
    print(call.sample.iid, call.abo_group, call.abo_genotype)

Genome builds

GRCh37/hg19, GRCh38/hg38, and T2T-CHM13v2 are supported. Build auto-detection uses marker coordinates and VCF header tokens such as ##reference=. Conflicting evidence returns an error requiring explicit --build.

Citations

Full records are printed by genoabo --method-info NAME and in the Citations section of each HTML run report.

• software — Yunye He. genoABO: genetically determined ABO blood group inference from genotype datasets. Version 0.3.1. 2026. https://github.com/cloufield/genoABO.
• common — Melzer D, Perry JRB, Hernandez D, Corsi AM, Stevens K, Rafferty I, et al. A genome-wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genet. 2008;4:e1000072. DOI: 10.1371/journal.pgen.1000072. PMID: 18464913.
• three-marker — Fry AE, Griffiths MJ, Auburn S, Diakite M, Forton JT, Green A, et al. Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malaria. Hum Mol Genet. 2008;17:567–576. DOI: 10.1093/hmg/ddm331. PMID: 18003641.
• ukb — UK Biobank. Data-Field 23165: Blood-type haplotype. https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=23165.
• extended — Daniels GL, Fletcher A, Garratty G, Henry S, Jørgensen J, Judd WJ, et al. Blood group terminology 2004: from the International Society of Blood Transfusion committee on terminology for red cell surface antigens. Vox Sang. 2004;87:304–316. DOI: 10.1111/j.1423-0410.2004.00564.x. PMID: 15585029.

See Inference methods for used-in and molecular-basis notes.

Documentation

Live site: https://cloufield.github.io/genoABO/

Preview the docs site locally:

pip install -e ".[docs]"
./serve.sh           # http://127.0.0.1:8000
zensical build       # writes ./site/

• Usage
• Inference methods
• Marker coordinates (includes 1000 Genomes LD r²)
• Assumptions and limitations
• Examples
• Update Log

License

MIT — see LICENSE.