new_benchmarks

inputs

@@ -1,5 +1,5 @@
 {
-  "{{ project_name }}.benchmarking_dir": "oss://chinese-quartet/quartet-result-data/NCTR_benchmarking_20181215/",
+  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",
   "{{ project_name }}.vcfstat.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.benchmark.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",

tasks/benchmark.wdl

@@ -28,13 +28,13 @@ task benchmark {
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.filtered.rtg.vcf.gz
 
 		if [ ${sample_mark} == "LCL5" ];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.afterfilterdiffbed.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [ ${sample_mark} == "LCL6" ]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.afterfilterdiffbed.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         elif [ ${sample_mark} == "LCL7" ]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.afterfilterdiffbed.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [ ${sample_mark} == "LCL8" ]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.afterfilterdiffbed.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi