diff --git a/bcbio/variation/strelka2.py b/bcbio/variation/strelka2.py
index <HASH>..<HASH> 100644
--- a/bcbio/variation/strelka2.py
+++ b/bcbio/variation/strelka2.py
@@ -188,8 +188,9 @@ def _af_annotate_and_filter(paired, items, in_file, out_file):
                 else:  # germline?
                     alt_counts = rec.format('AD')[:,1:]  # AD=REF,ALT1,ALT2,...
                     dp = np.sum(rec.format('AD')[:,0:], axis=1)
-                assert np.all(dp > 0), rec
-                af = np.true_divide(alt_counts, dp)
+                with np.errstate(divide='ignore', invalid='ignore'):  # ignore division by zero and put AF=.0
+                    af = np.true_divide(alt_counts, dp)
+                    af[~np.isfinite(af)] = .0  # -inf inf NaN -> .0
                 rec.set_format('AF', af)
                 if np.any(af[tumor_index] < min_freq):
                     vcfutils.cyvcf_add_filter(rec, 'MinAF')
Strelka2 AF calc: silent div by zero and replace AF=inf with AF=<I>