reference

inputs

@@ -1,5 +1,5 @@
 {
-  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_dataset_v4.0/",
+  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_dataset_v202011/",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.disk_size": "500",
   "{{ project_name }}.vcf_idx": "{{ vcf_idx }}",
@@ -8,3 +8,4 @@
   "{{ project_name }}.vcf": "{{ vcf }}",
   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }
+

tasks/benchmark.wdl

@@ -20,13 +20,13 @@ task benchmark {
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
 		if [[ ${sample} =~ "LCL5" ]];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL5.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.ref.v20201103.vcf.gz ${vcf} -f ${benchmarking_dir}/Quartet.callable.voted.collapse.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL6" ]]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL6.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.ref.v20201103.vcf.gz ${vcf} -f ${benchmarking_dir}/Quartet.callable.voted.collapse.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         elif [[ ${sample} =~ "LCL7" ]]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL7.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.ref.v20201103.vcf.gz ${vcf} -f ${benchmarking_dir}/Quartet.callable.voted.collapse.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL8" ]]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL8.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.ref.v20201103.vcf.gz ${vcf} -f ${benchmarking_dir}/Quartet.callable.voted.collapse.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi