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tasks/somaticFilter.wdl
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| @@ -18,7 +18,7 @@ task somaticFilter { | |||
| 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 | |||
| 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 | |||
| java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --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 { | |||
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