Bgen

1.9.9 verified Fri May 01 auth: no python

Python package for loading and manipulating data from BGEN files, a binary file format for storing genotype data. Current version is 1.9.9, compatible with Python >=3.8. It is actively maintained with periodic releases.

pip install bgen

Common errors

error ImportError: No module named 'bgen' ↓

cause Package not installed or installed in a different environment.

fix

Run 'pip install bgen' and ensure you're using the correct Python interpreter.

error bgen.BGENFile' object has no attribute 'read' ↓

cause Using an old API; BGENFile no longer has a read method; data is accessed via iteration or properties.

fix

Use iteration: for variant in bgen: ... or bgen[0] to access first variant.

error KeyError: 'rsid' ↓

cause Trying to access variant metadata using key-based access on a variant object, but variant is not a dict.

fix

Use dot notation: variant.rsid, variant.chromosome, etc.

Warnings

gotcha BGENFile indexing is 0-based, not 1-based. Often users expect variant positions to be 1-indexed. ↓

fix Always check documentation or use .rsid for identifiers.

deprecated Functions like 'bgen_open' are deprecated in favor of direct class instantiation. ↓

fix Use 'from bgen import BGENFile; bgen = BGENFile(filename)' instead.

gotcha Memory usage can be high when calling .genotype() on a large variant because it loads all sample data into memory. ↓

fix Use the 'subsample' or 'probs' arguments to subset or use iterator for large files.

Imports

BGENFile
```
from bgen import BGENFile
```
Main class for reading BGEN files.
BGENX
```
from bgen import BGENX
```
Class for indexing BGEN files.

Quickstart

Open a BGEN file and read basic information and variant genotypes.

from bgen import BGENFile

# Replace with your actual BGEN file path
bgen = BGENFile('example.bgen')

# Get number of samples
print('Number of samples:', bgen.nsamples)

# Get number of variants
print('Number of variants:', bgen.nvariants)

# Iterate over first 5 variants
for i, variant in enumerate(bgen):
    if i >= 5:
        break
    print('Variant:', variant.rsid, variant.chromosome, variant.position)
    # Access genotype probabilities (3D array: samples x alleles x ploidy)
    probs = variant.genotype()
    print('Genotype probs shape:', probs.shape)