add dp4 support in var into

jodyphelan · Oct 21, 2024 · ca1c11d · ca1c11d
1 parent 07a35b0
commit ca1c11d
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
@@ -23,6 +23,9 @@ def get_stand_support(var: pysam.VariantRecord,alt: str) -> Tuple[int,int]:
     elif 'SB' in var.samples[0]:
         forward_support = var.samples[0]['SB'][(alt_index+1)*2]
         reverse_support = var.samples[0]['SB'][(alt_index+1)*2+1]
+    elif 'DP4' in var.info:
+        forward_support = var.info['DP4'][alt_index*2]
+        reverse_support = var.info['DP4'][alt_index*2+1]
     else:
         forward_support = None
         reverse_support = None