Variant calling using Varscan somatic, processSomatic and somaticFilter based on BAM file.
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- task somaticFilter {
-
- String sample
- File varscan_snp_somatic_hc
- File varscan_snp_loh_hc
- File varscan_indel_somatic_hc
- File varscan_indel_loh_hc
- File varscan_indel
-
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Somatic.filter.vcf
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- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.LOH.filter.vcf
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- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf
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- java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${i}.indel.LOH.hc.vcf --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf
- >>>
-
- runtime {
- docker: docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
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- output {
- File varscan_snp_somatic_filter = "${sample}.VarScan.TN.SNP.Somatic.filter.vcf"
- File varscan_snp_loh_filter = "${sample}.VarScan.TN.SNP.LOH.filter.vcf"
- File varscan_indel_somatic_filter = "${sample}.VarScan.TN.INDEL.Somatic.filter.vcf"
- File varscan_indel_loh_filter = "${sample}.VarScan.TN.INDEL.LOH.filter.vcf"
- }
- }
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