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import hail as hl mt = hl.read_matrix_table('resources/post_qc.mt') mt = mt.filter_rows(hl.agg.call_stats(mt.GT, mt.alleles).AF[1] > 0.01) pca_scores = hl.hwe_normalized_pca(mt.GT, k = 5, True)[1] mt = mt.annotate_cols(pca = pca_scores[mt.s]) gwas = hl.linear_regression_rows( y=mt.pheno.caffeine_consumption, x=mt.GT.n_alt_alleles(), covariates=[1.0, mt.pheno.is_female, mt.pca.scores[0], mt.pca.scores[1], mt.pca.scores[2]]) p = hl.plot.manhattan(gwas.p_value) show(p) GWAS with Hail (click to show code ) Inst

GNU/Linux will also need the C and C++ standard libraries if not already installed.

Detailed instructions

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