.sample¶

Sample information file (.sample) accompanying .gen, .bgen genotype dosage files, or .haps phased reference panels. Loaded with --data/--sample, and produced by --export. The file is space-delimited with two header lines followed by one line per sample.

Overview¶

Field	Value
Format key	`bgen_sample`
Spec file	`formats/bgen_sample.json`
Cite name	Oxford/BGEN
Version	20260208
Last checked	20260208
Source	https://www.well.ox.ac.uk/~gav/qctool_v2/documentation/sample_file_formats.html
Source (2)	https://www.cog-genomics.org/plink/2.0/formats#sample
Citation	Band, G., & Marchini, J. (2018). BGEN: a binary file format for imputed genotype and haplotype data. bioRxiv.
## File layout

Field	Value
Separator	SPACE
NA value	NA
Header row	yes
Header lines	2
Second header line	Second header line specifies column types: '0' for ID/covariates, 'D' for discrete/categorical, 'B' for binary, 'P' for continuous phenotype
Column order	`ID_1`, `ID_2`, `missing`, `sex`
## Column mapping

Raw header	Canonical
`ID_1`	FID
`ID_2`	IID
`missing`	—
`sex`	SEX
## Header descriptions

Column	Description
`ID_1`	Family ID (header line 2 value: 0)
`ID_2`	Individual ID (header line 2 value: 0)
`missing`	Missing call frequency (header line 2 value: 0)
`sex`	Sex code ('1' = male, '2' = female, '0' = unknown; header line 2 value: D)
## Coverage

0/9 tier groups satisfied.

Tier	Status	Matched	Missing
Variant ID	no	—	SNPID, rsID
Genomic location	no	—	CHR, POS
Effect / other allele	no	—	EA, NEA
Effect size	no	—	BETA, OR, HR, Z
Uncertainty	no	—	SE
P-value	no	—	P, MLOG10P
Sample size	no	—	N, N_CASE
Allele frequency	no	—	EAF, MAF, NEAF
Imputation / QC	no	—	INFO
## See also