genoSecretor

genoSecretor infers genetically determined FUT2 secretor status from VCF, BGEN, PGEN, and PLINK genotype datasets.

pip install genosecretor
genosecretor biobank.pgen --out secretor

Research use only. genoSecretor is intended for population-genetics, epidemiology, GWAS, PheWAS, and biobank research. Genotype-inferred secretor status does not capture all rare or atypical FUT2 alleles and must not be used for clinical decision-making.

Quick start

genosecretor cohort.pgen --out secretor
# writes: secretor.secretor.tsv, secretor.qc.tsv, secretor.summary.txt, secretor.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 (./examples/run_synthetic.sh), plus 1000 Genomes FUT2 slices and an --assume-trans vs phase check.

Inspect markers without calling:

genosecretor cohort.pgen --inspect

Supported formats

Methods

genosecretor --methods
genosecretor --method-info two-marker
genosecretor data.pgen --method auto        # default
genosecretor data.pgen --ancestry eas      # require rs1047781; refuse `common` without it
genosecretor data.pgen --method two-marker
genosecretor data.pgen --method common
genosecretor data.pgen --method eas
genosecretor data.pgen --method proxy

Phenotypes: secretor, weak-secretor (Se^w/Se^w or Se^w/se), non-secretor (se/se). --phenotype-coding gwas recodes weak-secretor as non-secretor.

Options

--format auto|vcf|bcf|bgen|pgen|plink1
--build auto|hg19|hg38|chm13   # also GRCh37, GRCh38, CHM13v2, hs1
--method auto|two-marker|common|eas|proxy
--ancestry auto|eas|eur|afr|amr|unknown
--geno-mode auto|hardcall|dosage|probability
--phase auto|phased|unphased
--assume-trans / --no-assume-trans
--phenotype-coding biochemical|gwas
--min-genotype-prob 0.90
--dosage-hardcall-threshold 0.1
--strict-method
--inspect
--methods
--method-info NAME
--version
--report PATH.html

Full option list: docs/usage.md.

Python API

from genosecretor import SecretorCaller

caller = SecretorCaller(method="auto", ancestry="auto", build="auto")
result = caller.call("ukb.pgen")
for call in result.calls:
    print(call.sample.iid, call.secretor_status, call.fut2_genotype)

Genome builds

GRCh37/hg19, GRCh38/hg38, and T2T-CHM13v2 are supported. Build auto-detection uses marker coordinates, VCF header metadata, and chromosome lengths. Conflicting evidence returns an error requiring explicit --build.

Citations

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

• software — Yunye He. genoSecretor: genetically determined FUT2 secretor status inference from genotype datasets. Version 0.3.0. 2026. https://github.com/cloufield/genoSecretor.
• common — Kelly RJ, Rouquier S, Giorgi D, Lennon GG, Lowe JB. Sequence and expression of a candidate for the human Secretor blood group alpha(1,2)fucosyltransferase gene (FUT2). J Biol Chem. 1995;270:4640–4649. DOI: 10.1074/jbc.270.9.4640. PMID: 7876234.
• two-marker — Smyth DJ, Cooper JD, Howson JMM, et al. FUT2 nonsecretor status links type 1 diabetes susceptibility and resistance to infection. Diabetes. 2011;60:3081–3084. DOI: 10.2337/db11-0138. PMID: 22042020.
• eas — Koda Y, Soejima M, Liu Y, Kimura H. Molecular basis for secretor type α(1,2)-fucosyltransferase gene deficiency in a Japanese population. J Biol Chem. 1996;271:7410–7415. DOI: 10.1074/jbc.271.13.7410. PMID: 8631766.
• proxy — Barrett JC, Hansoul S, Nicolae DL, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008;40:955–962. DOI: 10.1038/ng.215. PMID: 18587394.

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

Documentation

https://cloufield.github.io/genoSecretor/

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.