mgp_extract_ld

Extract LD Blocks (mgp_extract_ld)

mgp_extract_ld extracts dense LD submatrices from pre-computed magenpy LD stores. LD stores can be provided as a single path or a glob.

mgp_extract_ld --help

Extract SNPs

mgp_extract_ld \
  --ld output/ld/chr_22/ \
  --snps rs123,rs456,rs789 \
  --output-file output/ld_block.csv

To read SNP IDs from a PLINK-style filter file:

mgp_extract_ld \
  --ld "output/ld/chr_*" \
  --snp-file variants.txt \
  --output-file output/ld_block.npz

Extract Regions

Regions can be specified directly:

mgp_extract_ld \
  --ld "output/ld/chr_*" \
  --region chr22:20000000-21000000,chr22:22000000-22500000 \
  --output-file output/ld_regions.csv

or through a BED-like file with chromosome, start, and end columns:

mgp_extract_ld \
  --ld "output/ld/chr_*" \
  --bed-file regions.bed \
  --output-file output/ld_regions.npy

Output Formats

The output format can be csv, npy, or npz. If --output-format auto is used, the format is inferred from the output file extension. Matrices are written as symmetric float32 arrays.

Use --log-level to control command-line logging.