IGV check

tasks/remove_IGVrm_bed.wdl

@@ -10,7 +10,11 @@ task remove_IGVrm_bed {
 
 	command <<<
 
-		cat ${bed_10X} ${PMRA_bed} | cut -f1,14,15 | sort -k1,1 -k2,2n > false.positive.bed
+		cat ${bed_10X} | cut -f1,13,14 > false.10X.bed
+
+		cat ${PMRA_bed} | cut -f1,14,15 > false.PMRA.bed
+
+		cat false.10X.bed false.PMRA.bed | sort -k1,1 -k2,2n > false.positive.bed
 
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools subtract -a ${benchmark_region} -b false.positive.bed > benchmark_regions.filtered.bed
 
@@ -24,7 +28,6 @@ task remove_IGVrm_bed {
 	}
 
 	output {
-		File variant_invariant = "variant_invariant.bed"
 		File benchmark_filtered_region = "benchmark_regions.filtered.bed"
 	}
 }