def concordance(): mt = get_mt() mt = mt.filter_rows(mt.alleles.length() == 2) g, r, c = hl.methods.qc.concordance(mt, mt, _localize_global_statistics=False) r._force_count() c._force_count()
def hwe_normalized_pca(): mt = get_mt() mt = mt.filter_rows(mt.info.AF[0] > 0.01) hl.hwe_normalized_pca(mt.GT)
def variant_qc(): hl.variant_qc(get_mt()).rows()._force_count()
def sample_qc(): hl.sample_qc(get_mt()).cols()._force_count()
def hwe_normalized_pca(): mt = get_mt() mt = mt.filter_rows(mt.info.AF[0] > 0.01) hl.hwe_normalized_pca(mt.GT)
def variant_qc(): hl.variant_qc(get_mt()).rows()._force_count()
def sample_qc(): hl.sample_qc(get_mt()).cols()._force_count()
def variant_and_sample_qc(): mt = get_mt() hl.sample_qc(hl.variant_qc(mt))._force_count_rows()