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variant-calling
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Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
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variant-calling/tasks/somaticFilter.wdl

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  1. task somaticFilter {

  2.   

  3.   String sample

  4.   File varscan_snp_somatic_hc

  5.   File varscan_snp_germline_hc

  6.   File varscan_snp_loh_hc

  7.   File varscan_indel_somatic_hc

  8.   File varscan_indel_germline_hc

  9.   File varscan_indel_loh_hc

  10.   File varscan_indel

  11. 

  12.   String docker

  13.   String cluster_config

  14.   String disk_size

  15. 

  16.   command <<<

  17.     java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Somatic.filter.vcf

  18. 

  19.     java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Germline.filter.vcf

  20. 

  21.     java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.LOH.filter.vcf

  22. 

  23.     java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf

  24. 

  25.     java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Germline.filter.vcf

  26. 

  27.     java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf

  28. 

  29.     # Merge SNP and INDEL

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

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

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

  33.   >>>

  34. 

  35.   runtime {

  36.     docker: docker

  37.     cluster: cluster_config

  38.     systemDisk: "cloud_ssd 40"

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

  40.   }

  41. 

  42.   output {

  43. 		File varscan_snp_somatic_filter = "${sample}.VarScan.TN.Somatic.filter.vcf"

  44.     File varscan_snp_germline_filter = "${sample}.VarScan.TN.Germline.filter.vcf"

  45. 		File varscan_snp_loh_filter = "${sample}.VarScan.TN.LOH.filter.vcf"

  46.   }

  47. }