Variant calling using Varscan somatic, processSomatic and somaticFilter based on BAM file.
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  1. task somatic {
  2. String sample
  3. File normal_bam
  4. File normal_bam_index
  5. File tumor_bam
  6. File tumor_bam_index
  7. File ref_dir
  8. String fasta
  9. String docker
  10. String cluster_config
  11. String disk_size
  12. command <<<
  13. samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx12g -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.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
  14. >>>
  15. runtime {
  16. docker: docker
  17. cluster: cluster_config
  18. systemDisk: "cloud_ssd 40"
  19. dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  20. }
  21. output {
  22. File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
  23. File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
  24. }
  25. }