virusbreakend: not using --skipsoftcliprealignment

PapenfussLab · Oct 14, 2021 · 28fd5fa · 28fd5fa
1 parent ac6a2ca
commit 28fd5fa
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scripts/virusbreakend b/scripts/virusbreakend
@@ -725,6 +725,7 @@ if [[ ! -f $file_gridss_vcf ]] ; then
 	write_status "Calling structural variants"
 	# backup metrics
 	for f in $(find $adjusteddir -name '*_metrics') ; do cp $f $f.bak ; done
+	# TODO: verify --skipsoftcliprealignment actually works
 	$timecmd gridss \
 		-w $adjusteddir \
 		-t $threads \
@@ -738,7 +739,6 @@ if [[ ! -f $file_gridss_vcf ]] ; then
 		--includeIndels false \
 		--includeSR false \
 		--includeDP false \
-		--skipsoftcliprealignment \
 		$gridssargs \
 		$bam_list_args \
 		1>&2 2>> $logfile