Update estimation of allele frequency

szhan · Mar 8, 2024 · da5bff6 · da5bff6
1 parent 7905759
commit da5bff6
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
@@ -963,8 +963,8 @@ def compute_allele_frequency(
     assert len(allele_probs_2) == n, "Lengths of alleles and probabilities differ."
     cum_ap_hap1 = np.sum(allele_probs_1[alleles_1 == allele])
     cum_ap_hap2 = np.sum(allele_probs_2[alleles_2 == allele])
-    cum_ap_total = np.sum(allele_probs_1) + np.sum(allele_probs_2)
-    est_af = (cum_ap_hap1 + cum_ap_hap2) / cum_ap_total
+    # See `printInfo` in `VcfRecBuilder.java` in BEAGLE 4.1 source code.
+    est_af = (cum_ap_hap1 + cum_ap_hap2) / (2 * n)
     return est_af