LUYAO REN
4 years ago
1 changed files with 4 additions and 4 deletions
+ 4
- 4
tasks/benchmark.wdl
View File
| @@ -25,13 +25,13 @@ 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.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 | |||
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