LD Clumping (clump)

Use graphld clump for p-value thresholding and LD-based pruning.

Basic Usage

uv run graphld clump \
    /path/to/sumstats.sumstats \
    output.tsv \
    --min-chisq 30 \
    --max-rsq 0.1

Clumping Options

Option	Default	Description
--min-chisq	30	Minimum chi-squared value for index-variant inclusion
--max-rsq	0.1	Maximum LD threshold for pruning

Inputs And Output

• Input summary statistics: .sumstats, .vcf/.vcf.gz, or .parquet; see Summary Statistics
• Output: a tab-separated file of retained index variants

All shared LDGM and runtime options from the CLI overview also apply here.