Variant calling using Varscan somatic, processSomatic and somaticFilter based on BAM file.
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- task processSomatic {
-
- String sample
- File varscan_snp
- File varscan_indel
-
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- cp ${varscan_snp} ./
- cp ${varscan_indel} ./
- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf
-
- >>>
-
- runtime {
- docker: docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
- File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
- File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
- File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
- File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
- File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
- File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
- File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
- File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
- File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
- File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
- File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
- }
- }
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