mgp_compute_ld

Compute LD Matrices (mgp_compute_ld)

mgp_compute_ld computes linkage-disequilibrium (LD) matrices from genotype data stored in PLINK BED format and writes magenpy Zarr LD stores.

mgp_compute_ld --help

Basic Usage

mgp_compute_ld \
  --bfile data/chr_22 \
  --estimator windowed \
  --ld-window-cm 3.0 \
  --output-dir output/ld_windowed/

The --bfile argument may point to a BED prefix or BED path. The command supports the windowed, block, shrinkage, and sample LD estimators. Estimator-specific arguments include:

• --ld-window, --ld-window-kb, --ld-window-cm for the windowed estimator.
• --ld-blocks for the block estimator.
• --genmap-Ne, --genmap-sample-size, and --shrinkage-cutoff for the shrinkage estimator.

Filtering

mgp_compute_ld \
  --bfile data/chr_22 \
  --estimator windowed \
  --ld-window-kb 1000 \
  --extract variants.txt \
  --keep samples.txt \
  --min-maf 0.01 \
  --output-dir output/ld/

--extract and --keep use PLINK-style filter files.

Storage And Logging

Use --storage-dtype, --compressor, and --compression-level to control LD storage. Use --log-level to control command-line logging:

mgp_compute_ld --bfile data/chr_22 --ld-window-cm 3 --output-dir output/ld --log-level INFO