LUYAO REN
5 lat temu
1 zmienionych plików z 2 dodań i 2 usunięć
+ 2
- 2
tasks/sister.wdl
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| ${family_name} ${LCL5_name} ${LCL7_name} ${LCL8_name} 2 -9" > ${family_name}.D5.ped | ${family_name} ${LCL5_name} ${LCL7_name} ${LCL8_name} 2 -9" > ${family_name}.D5.ped | ||||
| mkdir VBT_D5 | mkdir VBT_D5 | ||||
| /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_name}.vcf -father ${family_name}.vcf -child ${family_name}.vcf -pedigree ${family_name}.D5.ped -outDir D5 -out-prefix ${family_name}.D5 --output-violation-regions -thread-count $nt | |||||
| /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_name}.vcf -father ${family_name}.vcf -child ${family_name}.vcf -pedigree ${family_name}.D5.ped -outDir VBT_D5 -out-prefix ${family_name}.D5 --output-violation-regions -thread-count $nt | |||||
| # prepare ped file, D6 | # prepare ped file, D6 | ||||
| echo "${family_name} ${LCL8_name} 0 0 2 -9 | echo "${family_name} ${LCL8_name} 0 0 2 -9 | ||||
| ${family_name} ${LCL7_name} 0 0 1 -9 | ${family_name} ${LCL7_name} 0 0 1 -9 | ||||
| ${family_name} ${LCL6_name} ${LCL7_name} ${LCL8_name} 2 -9" > ${family_name}.D6.ped | ${family_name} ${LCL6_name} ${LCL7_name} ${LCL8_name} 2 -9" > ${family_name}.D6.ped | ||||
| mkdir VBT_D6 | mkdir VBT_D6 | ||||
| /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_name}.vcf -father ${family_name}.vcf -child ${family_name}.vcf -pedigree ${family_name}.D6.ped -outDir D6 -out-prefix ${family_name}.D6 --output-violation-regions -thread-count $nt | |||||
| /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_name}.vcf -father ${family_name}.vcf -child ${family_name}.vcf -pedigree ${family_name}.D6.ped -outDir VBT_D6 -out-prefix ${family_name}.D6 --output-violation-regions -thread-count $nt | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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