Surrogate Markers (surrogates)

Use graphld surrogates to precompute HDF5 surrogate-marker files for GWAS variants that are missing from LDGM references.

Basic Usage

uv run graphld surrogates \
    /path/to/sumstats.sumstats \
    surrogates.h5 \
    --population EUR

Inputs

Accepted inputs:

• .sumstats
• .vcf/.vcf.gz
• .parquet
• .snplist

Population

Surrogate lookup is population-specific. The CLI defaults to EUR; pass --population explicitly when precomputing surrogates for another population.

Output

The command writes an HDF5 file that can be passed back to graphld reml via --surrogates.

Use the shared runtime and metadata options from the CLI overview as needed.