Remove mpileup depth limit by default (connor-lab#63)

BCCDC-PHL · Jul 24, 2020 · 33b0f4c · 33b0f4c
1 parent 84a7abe
commit 33b0f4c
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/conf/illumina.config b/conf/illumina.config
@@ -33,8 +33,8 @@ params {
     // Sliding window quality threshold for keeping reads after primer trimming (illumina)
     illuminaQualThreshold = 20
 
-    // Mpileup depth for ivar
-    mpileupDepth = 100000
+    // Mpileup depth for ivar (although undocumented in mpileup, setting to zero removes limit)
+    mpileupDepth = 0
 
     // iVar frequency threshold for consensus variant (ivar consensus: -t)
     ivarFreqThreshold = 0.75