bed files

tasks/benchmark.wdl

@@ -27,9 +27,9 @@ task benchmark {
 	    elif [ ${sample_mark} == "LCL6" ]; then
 	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
         elif [ ${sample_mark} == "LCL7" ]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.bed.gz --threads $nt -o ${sample}
 	    elif [ ${sample_mark} == "LCL8" ]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.bed.gz --threads $nt -o ${sample}
         else
         	echo "only for quartet samples"
         fi