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  1. task mendelian {
  2. File sister_vcf
  3. File LCL7_vcf
  4. File LCL8_vcf
  5. String LCL7_name
  6. String LCL8_name
  7. String family_name
  8. File ref_dir
  9. String fasta
  10. String docker
  11. String cluster_config
  12. String disk_size
  13. command <<<
  14. export LD_LIBRARY_PATH=/opt/htslib-1.9
  15. mkdir VBT
  16. /opt/VBT-TrioAnalysis/vbt mendelian -ref ${ref_dir}/${fasta} -mother ${LCL8_vcf} -father ${LCL7_vcf} -child ${sister_vcf} -outDir VBT -out-prefix ${family_name} --output-violation-regions
  17. cat VBT/${family_name}_trio.vcf | grep '#' | cut -f1-9,10 > mother_header
  18. cat VBT/${family_name}_trio.vcf | grep -v '#' | cut -f1-9,10 | grep 'MD=1' | grep -v '0/0' | cat mother_header - > ${LCL8_name}.sister.mendelian.gt.vcf
  19. cat VBT/${family_name}_trio.vcf | grep '#' | cut -f1-9,11 > father_header
  20. cat VBT/${family_name}_trio.vcf | grep -v '#' | cut -f1-9,11 | grep 'MD=1' | grep -v '0/0' | cat father_header - > ${LCL7_name}.sister.mendelian.gt.vcf
  21. cat VBT/${family_name}_trio.vcf | grep '#' | cut -f1-9,12 > twin_header
  22. cat VBT/${family_name}_trio.vcf | grep -v '#' | cut -f1-9,12 | grep 'MD=1' | grep -v '0/0' | cat twin_header - > ${family_name}.twins.sister.mendelian.gt.vcf
  23. >>>
  24. runtime {
  25. docker:docker
  26. cluster: cluster_config
  27. systemDisk: "cloud_ssd 40"
  28. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  29. }
  30. output {
  31. Array[File] vbt_mendelian = glob("VBT/*")
  32. File mother_vcf = "${LCL8_name}.sister.mendelian.gt.vcf"
  33. File father_vcf = "${LCL7_name}.sister.mendelian.gt.vcf"
  34. File twins_vcf = "${family_name}.twins.sister.mendelian.gt.vcf"
  35. }
  36. }