Hello!
I read a vcf file of 1000 genomes data with hail. I combined it with my hail matrix table with union_cols to do PCA.
But when I ran eigenvalues, pcs, _ = hl.hwe_normalized_pca(combined.GT), it took a long time, I did not get results, and it said Ordering unsorted dataset with network shuffle.
I am confused about why it was ordering the dataset, and if there is a way to order it before running pca.
Thank you so much!