Fixed HMMCopy resolution settings for WGS

roland-rad-lab · Jun 28, 2020 · 60e06d9 · 60e06d9
1 parent 51ab53a
commit 60e06d9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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