benchmark files

defaults

@@ -1,5 +1,5 @@
 {
-  "benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",
+  "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_dataset_v202011/",
   "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
   "SENTIEON_LICENSE": "192.168.0.55:8990",
   "fasta": "GRCh38.d1.vd1.fa",

tasks/benchmark.wdl

@@ -34,13 +34,13 @@ task benchmark {
 		/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.afterfilterdiffbed.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.ref.v20201103.vcf.gz ${sample}.rtg.vcf.gz -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.afterfilterdiffbed.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.ref.v20201103.vcf.gz ${sample}.rtg.vcf.gz -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.afterfilterdiffbed.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.ref.v20201103.vcf.gz ${sample}.rtg.vcf.gz -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.afterfilterdiffbed.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.ref.v20201103.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.callable.voted.collapse.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi