Usage¶

Install genoSecretor and infer FUT2 secretor status from a genotype file. For pipeline internals see Workflow; for haplotype rules see Inference methods.

Install¶

pip install genosecretor

Quick start¶

genosecretor cohort.pgen --out secretor
# writes: secretor.secretor.tsv, secretor.qc.tsv, secretor.summary.txt, secretor.report.html

If --out is omitted, the prefix is the input path with its genotype suffix stripped (.vcf.gz and .vcf.bgz drop both suffixes, so eas_hg38.vcf.gz writes eas_hg38.secretor.tsv).

Command-line reference¶

genosecretor DATA [options]

--method auto picks the first ancestry-allowed method whose markers are present. Default --ancestry auto infers East Asian–like vs European-like from se428/se385 allele frequency when only one functional SNP is present (n ≥ 50): EAS-like files missing rs1047781 error instead of falling back to common; EUR-like files missing rs601338 error instead of falling back to eas. --ancestry unknown keeps the marker-presence hierarchy (two-marker → common → eas → proxy) and warns when common is chosen without rs1047781. Explicit --method still runs but warns if it contradicts ancestry. --phenotype-coding gwas recodes Se^w/Se^w and Se^w/se as non-secretor; fut2_genotype still keeps Se^w. See Inference methods.

--geno-mode auto uses GP, then DS, then hardcall GT. --phase auto uses phased haplotypes when the file has | genotypes; otherwise it enumerates unphased diplotypes. --build auto uses marker coordinates, header metadata, and chromosome lengths; conflicting evidence is an error and requires explicit --build.

Inspect and method metadata¶

genosecretor --version
genosecretor cohort.pgen --inspect
genosecretor --methods
genosecretor --method-info two-marker

--inspect reports which FUT2 tags were found, call rates, derived-allele frequencies, resolved ancestry, and the recommended method. Auto-selection that would mis-type an EAS-like or EUR-like cohort exits with status 1 after printing that table. --methods lists registered methods (two-marker, common, eas, proxy); auto is CLI selection, not a method. --methods and --method-info do not require an input file.

Input formats¶

GRCh37/hg19, GRCh38/hg38, and T2T-CHM13v2 are supported. --build GRCh38 (and the other aliases above) is equivalent to hg38.

Outputs¶

A successful call writes four files:

.secretor.tsv columns:

See Workflow for how genotypes move from file load to these files.

.qc.tsv is a metric/value table. Besides sample counts and marker call rates it includes ancestry_requested, ancestry_resolved, rs601338_lof_af, rs1047781_weak_af, and rs602662_proxy_af.

Python API¶

SecretorCaller constructor kwargs match the CLI. call() returns a CallerResult; iterate result.calls for per-sample fields.

from genosecretor import SecretorCaller

caller = SecretorCaller(
    method="auto",
    ancestry="auto",
    build="auto",
    genotype_mode="auto",
    phase="auto",
    format="auto",
    dosage_threshold=0.1,
    min_genotype_prob=0.9,
    strict_method=False,
    assume_trans=True,
    phenotype_coding="biochemical",
)
result = caller.call("ukb.pgen")
for call in result.calls:
    print(call.sample.iid, call.secretor_status, call.fut2_genotype)

Inspect without writing calls:

result = caller.call("ukb.pgen", inspect_only=True)
print(result.build, result.method, result.inspect)

See also¶

• Workflow — load-to-output pipeline
• Inference methods — haplotype and phenotype rules
• Markers — coordinates and 1000 Genomes LD r²
• Assumptions — limitations
• Examples — synthetic and 1000 Genomes demos