From c7f0b3cf1fa450226f4cfea8118ed94512343af6 Mon Sep 17 00:00:00 2001
From: Sam Chorlton <>
Date: Sat, 20 Jan 2024 21:08:49 -0800
Subject: [PATCH] Only count overlaps once

---
 tools/Varpipeline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/Varpipeline.py b/tools/Varpipeline.py
index 3bf27b1..db2fa98 100755
--- a/tools/Varpipeline.py
+++ b/tools/Varpipeline.py
@@ -266,7 +266,7 @@ def runCoverage(self):
         samDir = self.outdir + "/SamTools"
         i = datetime.now()
 
-        self.__CallCommand(['samtools depth', samDir + '/coverage.txt'],['samtools','depth', '-a', self.__finalBam])
+        self.__CallCommand(['samtools depth', samDir + '/coverage.txt'],['samtools','depth', '-s', '-a', self.__finalBam])
         #self.__CallCommand(['bedtools coverage', samDir + '/bed_amp_coverage.txt' ],
                            #[self.__bedtools, 'coverage', '-abam', self.__finalBam, '-b', self.__bedlist_amp])
         #self.__CallCommand(['sort', samDir + '/bed_amp_sorted_coverage.txt' ],['sort', '-nk', '6', samDir + '/bed_amp_coverage.txt'])