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Extract variants from DRAGEN BGEN file(s) into single BED file

Source: R/extract_variants.R
make_dragen_bed.Rd

For a given set of genomic coordinates extract the UK Biobank WGS DRAGEN variant calls (from the BGEN format, field 24309) into a single BED file.

This assumes your project has access to the WGS BGEN files released April 2025. If not, run `ukbrapR:::make_dragen_bed_from_pvcfs()` to use [tabix] and [plink] to subset the [DRAGEN WGS pVCF files].

Usage

make_dragen_bed(
  in_file,
  out_bed,
  progress = TRUE,
  verbose = FALSE,
  very_verbose = FALSE
)

Arguments

in_file

A data frame or file path. Contains at least two columns: `chr` and `pos` (in build 38). Other columns are ignored.

out_bed

A string.

progress

Logical. Show progress through each individual file, default=TRUE

verbose

Logical. Be verbose (show individual steps), default=FALSE

very_verbose

Logical. Be very verbose (show individual steps & show terminal output from Plink etc), default=FALSE

Value

A single merged BED file (and BIM and FAM files)

Author

Luke Pilling

Examples


make_dragen_bed(in_file=system.file("files", "pgs_liver_cirrhosis.txt", package="ukbrapR"), out_bed="liver_cirrhosis.dragen.variants")