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Convert UKB imputed BGEN files to PGEN on RAP

Source: R/grs.R
grs_bgen2pgen.Rd

Submits one Swiss Army Knife job per chromosome to the DNAnexus Research Analysis Platform, each converting a UKB imputed BGEN file to PGEN format with a MAF > 0.01 filter applied via plink2. Jobs run in parallel across chromosomes.

Usage

grs_bgen2pgen(
  chr = 1:22,
  dest = NULL,
  maf = 0.01,
  instance = "standard",
  priority = "low"
)

Arguments

chr

Integer vector. Chromosomes to process. Default: 1:22.

dest

Character scalar. RAP destination path for output PGEN files (e.g. "/pgen/"). Must be specified explicitly.

maf

Numeric scalar. Minor allele frequency filter passed to plink2 --maf. Variants with MAF below this threshold are excluded. Default: 0.01. Must be in (0, 0.5).

instance

Character scalar. Instance type preset: "standard" or "large". See Details. Default: "standard".

priority

Character scalar. Job priority: "low" or "high". Default: "low".

Value

A character vector of job IDs (one per chromosome), returned invisibly. Failed submissions are NA. Use job_ls, job_status, or job_wait to monitor progress.

Details

The function auto-generates the plink2 driver script, uploads it once to the RAP project root (/) on RAP, then loops over chr submitting one job per chromosome. A 500 ms pause between submissions prevents API rate-limiting.

Output path is critical. The driver script writes plink2 output to /home/dnanexus/out/out/ - the fixed path that Swiss Army Knife auto-uploads to dest on completion. Output files per chromosome: chr{N}_maf001.pgen/.pvar/.psam/.log.

Instance types:

"standard"

mem2_ssd1_v2_x4: 4 cores, 12 GB RAM. Suitable for smaller chromosomes (roughly chr 17–22).

"large"

mem2_ssd2_v2_x8: 8 cores, 28 GB RAM, 640 GB SSD. Required for large chromosomes (roughly chr 1–16) where standard storage is insufficient.

Examples

if (FALSE) { # \dontrun{
# Test with chr22 first (smallest chromosome)
ids <- grs_bgen2pgen(chr = 22, dest = "/pgen/", priority = "high")

# Small chromosomes - standard instance
ids_small <- grs_bgen2pgen(chr = 15:22, dest = "/pgen/")

# Large chromosomes - upgrade instance to handle storage
ids_large <- grs_bgen2pgen(chr = 1:16, dest = "/pgen/", instance = "large")

# Monitor
job_ls()
} # }