LUYAO REN
5 years ago
1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/sister.wdl
View File
| @@ -28,14 +28,14 @@ task sister { | |||
| ${family_name} ${LCL5_name} ${LCL7_name} ${LCL8_name} 2 -9" > ${family_name}.D5.ped | |||
| 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 $nt | |||
| # prepare ped file, D6 | |||
| echo "${family_name} ${LCL8_name} 0 0 2 -9 | |||
| ${family_name} ${LCL7_name} 0 0 1 -9 | |||
| ${family_name} ${LCL6_name} ${LCL7_name} ${LCL8_name} 2 -9" > ${family_name}.D6.ped | |||
| 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 { | |||
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