WIP: Dosage scores

szhan · Feb 25, 2024 · 53e2fd7 · 53e2fd7
1 parent dc22529
commit 53e2fd7
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
@@ -613,14 +613,15 @@ def compute_genotype_probs(alleles_1, allele_probs_1, alleles_2, allele_probs_2)
         gt_probs[i, 0] = ap_hap1_0 * ap_hap2_0  # P(00)
         gt_probs[i, 1] = ap_hap1_0 * ap_hap2_1 + ap_hap1_1 * ap_hap2_0  # P(01 or 10)
         gt_probs[i, 2] = ap_hap1_1 * ap_hap2_1  # P(11)
+        # dose[i] = gt_probs[i, 1] + gt_probs[i, 2]
     return gt_probs
 
 
 def compute_dosage_scores(alleles_1, allele_probs_1, alleles_2, allele_probs_2):
     """
     Compute dosage scores at ungenotyped positions of an individual.
 
-    In BEAGLE 4.1 output, DS: "Estimated ALT dose [P(RA) + P(AA)".
+    In BEAGLE 4.1 output, DS: "Estimated ALT dose [P(RA) + P(AA)]".
 
     :param numpy.ndarray alleles_1: Imputed alleles for haplotype 1.
     :param numpy.ndarray allele_probs_1: Imputed allele probabilities for haplotype 1.