Published December 6, 2024 | Version v1

.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. 

Files

GIANT_Extract_HGDP_1KG_Data.ipynb

Files (688.2 MB)

Name Size
md5:d59df100cad97c7cc622b9af64656bb5
59.1 kB Preview Download
md5:bc259f873f4b55158f0b448519a5b370
688.1 MB Download
md5:6824d4f4a43953c1d3284d220cc65155
57.5 kB Download