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()