bgen 1.0.2

Modern genetic association studies routinely employ data on tens to hundreds of thousands of individuals, genotyped or imputed at tens of millions of markers genome-wide.  Traditional data formats based on text representation of these data - such as the GEN format output by IMPUTE, or the Variant Call Format - are sometimes not well suited to these data quantities.  Indeed, for simple programs the time spent parsing these formats can dominate program execution time.

The binary GEN file format ("BGEN" format) which aims to address these problems. BGEN is a robust format that has been designed to have a specific blend of features that we believe make it useful for this type of study.  It is targetted for use with large, potentially imputed genetic datasets. Key features include:

  • The ability store both directly typed and imputed data.
  • The ability to store both unphased genotypes and phased haplotype data.
  • Small file sizes through the use of efficient, variable-precision packed bit representations and compression.
  • The use of per-variant compression makes the format simple to index and easy to catalogue.

Accessing the software

To load the module:

$ module load bgen/1.0.2-iomkl-2018a

To view command-line options for this application please run the following command with the module loaded:

$ bgenix -help

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the bgen website for more information regarding this application.

Last modified: 20 June 2018