From a0ea839f21fd6b4b5662a94239b5e1c2057d996b Mon Sep 17 00:00:00 2001
From: Charles Haynes <haynescd@chop.edu>
Date: Wed, 6 Nov 2024 09:44:33 -0500
Subject: [PATCH] Filter out Mutations with Status UnCalled for Counts

---
 .../persistence/mybatisclickhouse/StudyViewMapper.xml           | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
index fea1eb9853f..22b7724f997 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -42,6 +42,8 @@
         FROM genomic_event_derived
         <where>
             variant_type = 'mutation' AND
+            <!-- Mutation Status UnCalled is only used in Patient View to see how many supporting reads a variant might have in a sample -->
+            mutation_status != 'UNCALLED' AND
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
             </include>