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quartet_qc_vcf_input
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quartet_qc_vcf_input/tasks/benchmark.wdl

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  1. task benchmark {

  2. 	File vcf

  3. 	File benchmarking_dir

  4. 	File contig

  5. 	File sdf

  6. 	String project

  7. 	String sample = basename(vcf,".raw.vcf.gz")

  8. 	String docker

  9. 	String cluster_config

  10. 	String disk_size

  11. 

  12. 

  13. 	command <<<

  14. 		set -o pipefail

  15. 		set -e

  16. 		nt=$(nproc)

  17. 		mkdir -p /cromwell_root/tmp

  18. 		cp -r ${benchmarking_dir} /cromwell_root/tmp/

  19. 

  20. 		gunzip ${vcf} -c > unzip.vcf

  21. 		cat unzip.vcf | grep '#CHROM' > name

  22. 		cat unzip.vcf | grep -v '#' > body

  23. 		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered

  24. 

  25. 		if grep -q PASS "body.filtered"; then

  26. 			cat body.filtered | grep -v '0/0' | grep 'PASS' > body.filtered.gt

  27. 			cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered.gt > filtered.vcf

  28. 		else

  29. 			cat body.filtered | grep -v '0/0' > body.filtered.gt

  30. 			cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered.gt > filtered.vcf

  31. 		fi			

  32. 

  33. 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5" > LCL5_name

  34. 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL6" > LCL6_name

  35. 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL7" > LCL7_name

  36. 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL8" > LCL8_name

  37. 

  38. 

  39. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip filtered.vcf -c > ${project}.${sample}.rtg.vcf.gz

  40. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.rtg.vcf.gz

  41. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${project}.${sample}.rtg.vcf.gz -o ${sample}.rtg.SNV.vcf.gz --snps-only

  42. 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${project}.${sample}.rtg.vcf.gz -o ${sample}.rtg.INDEL.vcf.gz --non-snps-only

  43. 

  44. 

  45. 		if [[ ${sample} =~ "LCL5" ]];then

  46. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.SNV.vcf.gz -c ${sample}.rtg.SNV.vcf.gz -o ${sample}_SNV -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  47. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  48. 			cat filtered.vcf | grep '##' > header

  49. 			cat filtered.vcf | grep -v '#' > body

  50. 			cat header LCL5_name body > LCL5.vcf

  51. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL5.vcf -c > ${project}.${sample}.reformed.vcf.gz

  52. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz

  53. 	    elif [[ ${sample} =~ "LCL6" ]]; then

  54. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.SNV.vcf.gz -c ${sample}.rtg.SNV.vcf.gz -o ${sample}_SNV -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  55. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  56. 			cat filtered.vcf | grep '##' > header

  57. 			cat filtered.vcf | grep -v '#' > body

  58. 			cat header LCL6_name body > LCL6.vcf

  59. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL6.vcf -c > ${project}.${sample}.reformed.vcf.gz

  60. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz

  61.         elif [[ ${sample} =~ "LCL7" ]]; then

  62. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.SNV.vcf.gz -c ${sample}.rtg.SNV.vcf.gz -o ${sample}_SNV -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  63. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  64. 			cat filtered.vcf | grep '##' > header

  65. 			cat filtered.vcf | grep -v '#' > body

  66. 			cat header LCL7_name body > LCL7.vcf

  67. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL7.vcf -c > ${project}.${sample}.reformed.vcf.gz

  68. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz

  69. 	    elif [[ ${sample} =~ "LCL8" ]]; then

  70. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.SNV.vcf.gz -c ${sample}.rtg.SNV.vcf.gz -o ${sample}_SNV -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  71. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed

  72. 			cat filtered.vcf | grep '##' > header

  73. 			cat filtered.vcf | grep -v '#' > body

  74. 			cat header LCL8_name body > LCL8.vcf

  75. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL8.vcf -c > ${project}.${sample}.reformed.vcf.gz

  76. 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz

  77.         else

  78.         	echo "only for quartet samples"

  79.         fi		

  80. 

  81. 

  82.         cat ${sample}_SNV/summary.txt > ${project}.${sample}_SNV_precision_recall.txt

  83.         cat ${sample}_INDEL/summary.txt > ${project}.${sample}_INDEL_precision_recall.txt

  84.         

  85. 	>>>

  86. 

  87. 	runtime {

  88. 		docker:docker

  89. 		cluster:cluster_config

  90. 		systemDisk:"cloud_ssd 40"

  91. 		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"

  92. 	}

  93. 

  94. 	output {

  95. 		File rtg_vcf = "${project}.${sample}.reformed.vcf.gz"

  96. 		File rtg_vcf_index = "${project}.${sample}.reformed.vcf.gz.tbi"

  97. 		File SNV_result = "${project}.${sample}_SNV_precision_recall.txt"

  98. 		File Indel_result = "${project}.${sample}_INDEL_precision_recall.txt"

  99. 	}

  100. }