Variant calling using Varscan somatic, processSomatic and somaticFilter based on BAM file.
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  1. task processSomatic {
  2. String sample
  3. File varscan_snp
  4. File varscan_indel
  5. String docker
  6. String cluster_config
  7. String disk_size
  8. command <<<
  9. java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${varscan_snp}
  10. java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${varscan_indel}
  11. >>>
  12. runtime {
  13. docker: docker
  14. cluster: cluster_config
  15. systemDisk: "cloud_ssd 40"
  16. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  17. }
  18. output {
  19. File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
  20. File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
  21. File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
  22. File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
  23. File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
  24. File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
  25. File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
  26. File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
  27. File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
  28. File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
  29. File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
  30. File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
  31. }
  32. }