Published December 6, 2024
| Version v1
Dataset
Open
.bed / .bim / .fam files for HGDP + 1KG data from gnomAD
Authors/Creators
Description
From the gnomAD v3.1.2 release, we pull the HGDP + 1KG dataset. We drop related samples, & retain variants with AF > 1% & p-value of HWE < 10^(-12). This is done using Hail, with code available in the file GIANT_Extract_HGDP_1KG_Data.ipynb. The super population label file was generated by gnomAD.
We plan to use this dataset to train ML algorithms that will assign ancestry labels if required during downstream analysis.