From b29e9281ada09aa2cd1f8ae643102467705ac8d4 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 23 Sep 2019 14:19:31 +0200
Subject: [PATCH] reverted the MQ filter

---
 protocols/SnpFiltration.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/protocols/SnpFiltration.sh b/protocols/SnpFiltration.sh
index a420b743..6d9794a1 100755
--- a/protocols/SnpFiltration.sh
+++ b/protocols/SnpFiltration.sh
@@ -30,8 +30,8 @@ java -XX:ParallelGCThreads=1 -Djava.io.tmpdir="${tempDir}" -Xmx4g -jar "${EBROOT
 --variant "${sampleVariantsMergedSnpsVcf}" \
 --filterExpression "QD < 2.0" \
 --filterName "filterQD_lt2.0" \
---filterExpression "MQ < 40.0" \
---filterName "filterMQ_lt40.0" \
+--filterExpression "MQ < 25.0" \
+--filterName "filterMQ_lt25.0" \
 --filterExpression "SOR > 3.0" \
 --filterName "filterSOR_gt3.0" \
 --filterExpression "MQRankSum < -12.5" \