cellink.resources.get_1000genomes_hapmap3

cellink.resources.get_1000genomes_hapmap3(config_path='./cellink/resources/config/1000genomes.yaml', data_home=None, refresh=False)

Download the HapMap3 SNP list (no MHC region).

Used as --print-snps when computing per-annotation LD scores to restrict output to well-imputed HapMap3 SNPs, and as --merge-alleles during sumstats munging.

Downloaded from Zenodo record 10515792 (hm3_no_MHC.list.txt).

Parameters:

• config_path (str or pathlib.Path) – Path to YAML configuration file.

• data_home (str or pathlib.Path, optional) – Root directory where data will be stored.

• refresh (bool, default=False) – If True, re-downloads the file even if it already exists.

Return type:

Path

Returns:

pathlib.Path Path to the downloaded hm3_no_MHC.list.txt file.

Examples

>>> hapmap3_snps = get_1000genomes_hapmap3()
>>> print_snps = str(hapmap3_snps)  # passed as --print-snps to ldsc.py