YaqingLiu
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WesPipe
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Automated integrated analysis software for genomics data of the cancer patients.
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WesPipe/tasks/VarScan.wdl

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  1. task VarScan {

  2. 

  3.   String sample

  4.   File normal_bam

  5.   File normal_bam_index

  6.   File tumor_bam

  7.   File tumor_bam_index

  8. 

  9.   File ref_dir

  10.   String fasta

  11.   String docker

  12.   String cluster_config

  13.   String disk_size

  14. 

  15.   command <<<

  16.     # somatic

  17.     samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.SNP --output-indel ${sample}.VarScan.INDEL --strand-filter 1

  18. 

  19.     # processSomatic

  20.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf

  21.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf

  22. 

  23.     # somaticFilter

  24.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.SNP.Somatic.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${sample}.VarScan.INDEL.vcf --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf

  25.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.SNP.Germline.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${sample}.VarScan.INDEL.vcf --output-file ${sample}.VarScan.SNP.Germline.filter.vcf

  26.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.SNP.LOH.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${sample}.VarScan.INDEL.vcf --output-file ${sample}.VarScan.SNP.LOH.filter.vcf

  27.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.INDEL.Somatic.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Somatic.filter.vcf

  28.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.INDEL.Germline.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Germline.filter.vcf

  29.     java -Xmx64g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${sample}.VarScan.INDEL.LOH.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.LOH.filter.vcf

  30. 

  31.     # Merge SNP and INDEL

  32.     awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.Somatic.vcf

  33.     awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Germline.filter.vcf | cat ${sample}.VarScan.INDEL.Germline.filter.vcf - > ${sample}.VarScan.Germline.vcf

  34.     awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.LOH.filter.vcf | cat ${sample}.VarScan.INDEL.LOH.filter.vcf - > ${sample}.VarScan.LOH.vcf

  35.   >>>

  36.   

  37.   runtime {

  38.     docker: docker

  39.     cluster: cluster_config

  40.     systemDisk: "cloud_ssd 40"

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

  42.   }

  43.   

  44.   output {

  45.     File varscan_snp = "${sample}.VarScan.SNP.vcf"

  46.     File varscan_indel = "${sample}.VarScan.INDEL.vcf"

  47. 		File varscan_somatic = "${sample}.VarScan.Somatic.vcf"

  48.     File varscan_germline = "${sample}.VarScan.Germline.vcf"

  49. 		File varscan_loh = "${sample}.VarScan.LOH.vcf"

  50.   }

  51. }