YaqingLiu
/
Varscan2
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Variant calling using Varscan somatic, processSomatic and somaticFilter based on BAM file.
Nevar pievienot vairāk kā 25 tēmas Tēmai ir jāsākas ar burtu vai ciparu, tā var saturēt domu zīmes ('-') un var būt līdz 35 simboliem gara.
14 Revīzijas
1 Atzars
Atzars: master
Atzari Tagi
${ item.name }
Izveidot atzaru ${ searchTerm }
no 'master'
${ noResults }
Varscan2/tasks/processSomatic.wdl

40 rindas
1.5KB
Neapstrādāts Patstāvīgā saite Vainot Vēsture 

  1. task processSomatic {

  2.     

  3.     String sample

  4.     File varscan_snp

  5.     File varscan_indel

  6.     

  7.     String docker

  8.     String cluster_config

  9.     String disk_size

  10. 

  11.     command <<<

  12.         cp ${varscan_snp} ./

  13.         cp ${varscan_indel} ./

  14.         java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf

  15.         java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf

  16. 

  17.     >>>

  18. 

  19.     runtime {

  20.         docker: docker

  21.         cluster: cluster_config

  22.         systemDisk: "cloud_ssd 40"

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

  24.     }

  25. 

  26.     output {

  27.         File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"

  28.         File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"

  29.         File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"

  30.         File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"

  31.         File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"

  32.         File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"

  33.         File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"

  34.         File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"

  35.         File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"

  36.         File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"

  37.         File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"

  38.         File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"

  39.     }

  40. }