reference datasets

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.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.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 ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.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 ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.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 ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi