admix.cli.admix_grm#

admix.cli.admix_grm(pfile: str, out_prefix: str, maf_cutoff: float = 0.005, her_model='mafukb', freq_cols=['LANC_FREQ1', 'LANC_FREQ2'], snp_chunk_size: int = 256, snp_list: str | None = None, write_raw: bool = False) → None[source]#

Calculate the admix GRM for a given pfile

Parameters:

  • pfile (str) – Path to the pfile

  • out_prefix (str) – Prefix of the output files

  • maf_cutoff (float, optional) – MAF cutoff for the admixed individuals, by default 0.005

  • her_model (str, optional) – Heritability model, by default “mafukb” one of “uniform”, “gcta”, “ldak”, “mafukb”

  • freq_cols (List[str], optional) – Columns of the pfile to use as frequency, by default [“LANC_FREQ1”, “LANC_FREQ2”] to perform the ancestry-specific MAF cutoffs

  • snp_chunk_size (int, optional) – Number of SNPs to read at a time, by default 256 This can be tuned to reduce memory usage

  • snp_list (str, optional) – Path to a file containing a list of SNPs to use. Each line should be a SNP ID. Only SNPs in the list will be used for the analysis. By default None

  • write_raw (bool, optional) – Whether to write the raw GRM, G1, G2, G12, by default False

Returns:

  • GRM files ({out_prefix}.[K1, K2].[grm.bin | grm.id | grm.n] will be generated)

  • Weight file ({out_prefix}.weight.tsv will be generated)