union

tasks/final_merge.wdl

@@ -10,7 +10,7 @@ task final_merge {
 
 	command <<<
 
-		/opt/ccdg/bedtools-2.27.1/bin/bedtools merge -i ${HR_merged_intersect_bed} ${variants_merged_bed} > variant_invariant.bed
+		cat ${HR_merged_intersect_bed} ${variants_merged_bed} | sort -k1,1 -k2,2n | /opt/ccdg/bedtools-2.27.1/bin/bedtools merge -i - > variant_invariant.bed
 
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools intersect -a variant_invariant.bed -b ${callable_merged_intersect_bed} > benchmark_regions.bed