cellink.tl.external.bedgraph_to_snp_annotation

cellink.tl.external.bedgraph_to_snp_annotation(bedgraph, bim_file, out_prefix, *, use_bedtools=True)

Convert a bedgraph file to an S-LDSC annotation file (.annot.gz).

Implements the logic of GSSG’s bedgraph_to_annot.py. Each SNP in the BIM file is assigned the score of the bedgraph interval it falls within (0 if not covered).

Parameters:

• bedgraph (DataFrame | str | Path) – Bedgraph DataFrame with columns (chr, start, end, score), or path to file.

• bim_file (str | Path) – PLINK BIM file defining SNP positions.

• out_prefix (str) – Output prefix; the file {out_prefix}.annot.gz is written.

• use_bedtools (bool (default: True)) – If True and bedtools is available, use bedtools intersect (more robust). Otherwise falls back to pure-Python interval lookup.

Return type:

Path

Returns:

Path Path to the written annotation file.