bedtools location

tasks/gvcf_homo_ref.wdl

@@ -11,7 +11,7 @@ task gvcf_homo_ref {
 
 		awk '{ if ($5 == "<NON_REF>") { print } }'  ${gvcf} | sed s'/:/\t/'g | awk '{ if($16 >= 30) { print }}' | cut -f1,2,8 | sed s'/END=//g' > ${sample}.filtered.bed
 
-		bedtools merged -i ${sample}.filtered.bed > ${sample}.homo_ref.bed 
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools merged -i ${sample}.filtered.bed > ${sample}.homo_ref.bed 
 
 		>>>