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version 1.0
task VarDict {
input {
String? installDir
File tumorBam
File normalBam
File refFasta
File bedFile
String tumorSampleName
String normalSampleName
String outputVcf
Int chromosomeColumn = 1
Int startColumn = 2
Int endColumn = 3
Int geneColumn = 4
String? preCommand
}
String toolCommand = if defined(installDir)
then installDir + "/VarDict"
else "vardict"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
-G ~{refFasta} \
-N ~{tumorSampleName} \
-b "~{tumorBam}|~{normalBam}" \
-c ~{chromosomeColumn} \
-S ~{startColumn} \
-E ~{endColumn} \
-g ~{geneColumn} \
~{bedFile} | \
~{installDir + "/"}testsomatic.R | \
~{installDir + "/"}var2vcf_paired.pl \
-N "~{tumorSampleName}|~{normalSampleName}" \
> ~{outputVcf}
}
output {
File vcfFile = outputVcf
}
}