From 4868bd7fa81f367bc35ecb9dff632bd2e78ffe8e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 22 Apr 2020 08:13:50 -0500
Subject: [PATCH] upgrading to msi pro
---
variants/msisensor.sh | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/variants/msisensor.sh b/variants/msisensor.sh
index db133b1..1ab0aba 100755
--- a/variants/msisensor.sh
+++ b/variants/msisensor.sh
@@ -41,9 +41,8 @@ fi
if [[ -n $normal ]]
then
-
msisensor-pro msi -d ${index_path}/microsatellites.list -n $normal -t $sbam -o ${pair_id}.msi $bedopt
else
# -M ${index_path}/msi_tumoronly_model
- msisensor2 msi -d ${index_path}/microsatellites.list -t $sbam -o ${pair_id}.msi $bedopt
+ msisensor-pro pro -d ${index_path}/microsatellites.list_baseline -t ${sbam} -o ${pair_id}.msi $bedopt
fi
--
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