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looking for 1000g hg38 reference data to anchor with my genomic data to plot the principal components

Hello

I'm performing my first GWAS and I am trying to plot the principal components of my data by anchoring them to a reference data by ancestry. However, I'm having a very hard time finding a reference on build 38 with individual-level data, rsIDs, and ancestry.

I have only been able to access older versions of reference data, and when I have tried lifting over to hg38 I have to create a readable "txt" bed file however I'm having a hard time converting this bed txt file back to a binary file which is needed for the plink PCA commands.

Does anyone know how I could access this data from the 1000 genomes project in GRCh38 build? Preferably in PLINK or VCF format. This would make my pipeline much more streamlined.

gwas hg38 principal-components
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updated by chrchang523 chrchang523 • written by nicole • nicole

3 answers

This is available on the PLINK 2 resources page: https://www.cog-genomics.org/plink/2.0/resources#phase3_1kg

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written by chrchang523 chrchang523

You can find the 1000 Genomes high coverage GRCh 38 dataset here: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/

The dataset is described in detail here: https://doi.org/10.1016/j.cell.2022.08.004

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written by DBScan • DBScan

If you are just trying to project your samples onto a 1kg-derived PCA, you can do this in TileDB Cloud. If you sign up there we can get you some credits and assistance with your queries.

The following notebook outlines how that would take place:

TileDB PCA on DRAGEN 1kg

pca plus test samples

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written by Jeremy Leipzig Jeremy Leipzig

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