LUYAO REN
4 年之前
共有 1 個文件被更改，包括 2 次插入 和 2 次删除
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tasks/mendelian.wdl
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| mkdir VBT_D5_outside | mkdir VBT_D5_outside | ||||
| /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf_outside} -father ${family_vcf_outside} -child ${family_vcf_outside} -pedigree ${family_name}.D5.ped -outDir VBT_D5_outside -out-prefix ${family_name}.D5.outside --output-violation-regions -thread-count $nt | /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf_outside} -father ${family_vcf_outside} -child ${family_vcf_outside} -pedigree ${family_name}.D5.ped -outDir VBT_D5_outside -out-prefix ${family_name}.D5.outside --output-violation-regions -thread-count $nt | ||||
| cat VBT_D5_inside/${family_name}.D5.outside_trio.vcf > ${family_name}.D5.outside.vcf | |||||
| cat VBT_D5_outside/${family_name}.D5.outside_trio.vcf > ${family_name}.D5.outside.vcf | |||||
| echo -e "${family_name}\tLCL8\t0\t0\t2\t-9\n${family_name}\tLCL7\t0\t0\t1\t-9\n${family_name}\tLCL6\tLCL7\tLCL8\t2\t-9" > ${family_name}.D6.ped | echo -e "${family_name}\tLCL8\t0\t0\t2\t-9\n${family_name}\tLCL7\t0\t0\t1\t-9\n${family_name}\tLCL6\tLCL7\tLCL8\t2\t-9" > ${family_name}.D6.ped | ||||
| mkdir VBT_D6_outside | mkdir VBT_D6_outside | ||||
| /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf_outside} -father ${family_vcf_outside} -child ${family_vcf_outside} -pedigree ${family_name}.D6.ped -outDir VBT_D6_outside -out-prefix ${family_name}.D6.outside --output-violation-regions -thread-count $nt | /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${family_vcf_outside} -father ${family_vcf_outside} -child ${family_vcf_outside} -pedigree ${family_name}.D6.ped -outDir VBT_D6_outside -out-prefix ${family_name}.D6.outside --output-violation-regions -thread-count $nt | ||||
| cat VBT_D6_inside/${family_name}.D6.outside_trio.vcf > ${family_name}.D6.outside.vcf | |||||
| cat VBT_D6_outside/${family_name}.D6.outside_trio.vcf > ${family_name}.D6.outside.vcf | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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