LUYAO REN
vor 4 Jahren
2 geänderte Dateien mit 5 neuen und 5 gelöschten Zeilen
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defaults
Datei anzeigen
| { | { | ||||
| "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_INSTALL_DIR": "/opt/sentieon-genomics", | ||||
| "SENTIEON_LICENSE": "192.168.0.55:8990", | "SENTIEON_LICENSE": "192.168.0.55:8990", | ||||
| "fasta": "GRCh38.d1.vd1.fa", | "fasta": "GRCh38.d1.vd1.fa", |
+ 4
- 4
tasks/benchmark.wdl
Datei anzeigen
| /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz | /opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz | ||||
| if [[ ${sample} =~ "LCL5" ]];then | 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 | 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 | 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 | 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 | else | ||||
| echo "only for quartet samples" | echo "only for quartet samples" | ||||
| fi | fi |
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