From 60e06d9bdc5bd9f678caee8101f53fd181313350 Mon Sep 17 00:00:00 2001
From: Sebastian Lange <sebastian.lange@tum.de>
Date: Sun, 28 Jun 2020 10:11:01 +0200
Subject: [PATCH] Fixed HMMCopy resolution settings for WGS

---
 MoCaSeq.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/MoCaSeq.sh b/MoCaSeq.sh
index 8e36bf6..ed54702 100755
--- a/MoCaSeq.sh
+++ b/MoCaSeq.sh
@@ -873,13 +873,13 @@ fi
 echo '---- Generate and plot copy number data ----' | tee -a $name/results/QC/$name.report.txt
 echo -e "$(date) \t timestamp: $(date +%s)" | tee -a $name/results/QC/$name.report.txt
 
+resolution=20000
+
 if [ $sequencing_type = 'WES' ]; then
 
 	echo '---- Run CopywriteR ----' | tee -a $name/results/QC/$name.report.txt
 	echo -e "$(date) \t timestamp: $(date +%s)" | tee -a $name/results/QC/$name.report.txt
 
-	resolution=20000
-
 	Rscript $repository_dir/CNV_RunCopywriter.R $name $species $threads $runmode $genome_dir $centromere_file $varregions_file $resolution $types
 
 	echo '---- Export raw data and re-normalize using Mode ----' | tee -a $name/results/QC/$name.report.txt