cellink.resources.merge_1000g_plink_chromosomes

cellink.resources.merge_1000g_plink_chromosomes(plink_dir, prefix, output_prefix, chromosomes=None, plink_cmd='plink')

Merge per-chromosome 1000G PLINK bfiles into a single genome-wide bfile.

Convenience wrapper for the standard PLINK merge workflow needed before passing a reference panel to write_slurm_array_job(). The resulting .bed/.bim/.fam files can be passed directly as plink_bfile.

Skips the merge if the output .bed file already exists.

Parameters:

• plink_dir (str or Path) – Directory containing the per-chromosome bfiles, as returned by get_1000genomes_plink_files().

• prefix (str) – Filename prefix of the per-chromosome files (e.g. "1000G.EUR.QC." so that chromosome 1 is 1000G.EUR.QC.1.bed).

• output_prefix (str or Path) – Prefix for the merged output (e.g. "data/1000G_EUR_merged"). PLINK appends .bed, .bim, .fam.

• chromosomes (list of int, optional) – Chromosomes to include. Defaults to autosomes 1-22.

• plink_cmd (str, default="plink") – PLINK 1.9 executable name or full path.

Return type:

Path

Returns:

Path output_prefix as a Path (without extension).

Examples

>>> plink_dir, prefix = get_1000genomes_plink_files(population="EUR")
>>> bfile = merge_1000g_plink_chromosomes(plink_dir, prefix, "data/1000G_EUR_merged")
>>> # Pass bfile to write_slurm_array_job(plink_bfile=bfile, ...)