Recode allele to print in VCF

szhan · Feb 26, 2024 · 176a5a4 · 176a5a4
1 parent 099d773
commit 176a5a4
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
@@ -864,8 +864,8 @@ def write_vcf(ref_ts, impdata, out_file, chr_name="1"):
             line_str = chr_name + "\t"
             line_str += str(int(impdata.site_pos[i])) + "\t"
             line_str += str(i) + "\t"
-            REF = impdata.get_ref_allele_at_site(i)
-            ALT = impdata.get_alt_allele_at_site(i)
+            REF = _ACGT_ALLELES[impdata.get_ref_allele_at_site(i)]
+            ALT = _ACGT_ALLELES[impdata.get_alt_allele_at_site(i)]
             line_str += REF + "\t"
             line_str += ALT + "\t"
             # QUAL