mgp_expand_ld

Expand Variants By LD (mgp_expand_ld)

mgp_expand_ld expands a focal SNP list to include variants in LD with those SNPs using pre-computed magenpy LD matrices. The LD threshold is provided as an R-squared threshold with --r2-threshold.

mgp_expand_ld --help

Basic Usage

mgp_expand_ld \
  --ld "output/ld/chr_*" \
  --snp-file focal_snps.txt \
  --r2-threshold 0.1 \
  --output-file output/expanded_variants.tsv

The SNP file is read as a PLINK-style filter file. Use --snp-column to select a zero-based SNP column index. The output includes the focal SNPs and all LD neighbors that meet the threshold.

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