Variant calling using Varscan somatic, processSomatic and somaticFilter based on BAM file.
Nie możesz wybrać więcej, niż 25 tematów
Tematy muszą się zaczynać od litery lub cyfry, mogą zawierać myślniki ('-') i mogą mieć do 35 znaków.
|
- task processSomatic {
-
- String sample
- File varscan_snp
- File varscan_indel
-
- File ref_dir
- String fasta
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${varscan_snp}
- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${varscan_indel}
- >>>
-
- runtime {
- docker: docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
- File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
- File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
- File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
- }
- }
|
