From 33b0f4c9c07cd536a8abed59c925a79d66f4b83e Mon Sep 17 00:00:00 2001
From: Matt Bull <bullmj2@gmail.com>
Date: Fri, 24 Jul 2020 16:32:56 +0000
Subject: [PATCH] Remove mpileup depth limit by default (#63)

---
 conf/illumina.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/illumina.config b/conf/illumina.config
index bd82749e..4b39d48a 100644
--- 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