handle missing or zero depth field in tumor

genome · Jun 17, 2019 · 0e40685 · 0e40685
1 parent e4850ef
commit 0e40685
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/somatic_llr_filter.py b/somatic_llr_filter.py
@@ -319,7 +319,12 @@ def missingVals(arr):
             if error_expect == 1:
                 error_expect = 1 - args.sequence_error_rate
 
-            tumor_freq = tumor_var/tumor_depth
+            #handle case where depth is zero or missing
+            if tumor_depth == 0:
+                tumor_freq = 0
+            else:
+                tumor_freq = tumor_var/tumor_depth
+
             if tumor_freq == 0:
                 tumor_freq = args.sequence_error_rate
             elif tumor_freq == 1: