reference 4.0

inputs

 {
-  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",
+  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_dataset_v4.0/",
   "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",

tasks/benchmark.wdl

 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
 
 		if [[ ${sample} =~ "LCL5" ]];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.voted.mendelian.lcr.centromere.homopolyer.sv.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.highconfidence.lcr.centromere.homopolyer.sv.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.voted.mendelian.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL6" ]]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.voted.mendelian.lcr.centromere.homopolyer.sv.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.highconfidence.lcr.centromere.homopolyer.sv.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.voted.mendelian.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         elif [[ ${sample} =~ "LCL7" ]]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.voted.mendelian.lcr.centromere.homopolyer.sv.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.highconfidence.lcr.centromere.homopolyer.sv.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.voted.mendelian.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL8" ]]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.voted.mendelian.lcr.centromere.homopolyer.sv.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.highconfidence.lcr.centromere.homopolyer.sv.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.voted.mendelian.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi