Commit 5ff67b19 authored by Peter van 't Hof's avatar Peter van 't Hof

Added option to skip AnalyzeCovariates

parent e69b6f0c
......@@ -213,11 +213,13 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
add(baseRecalibrator)
val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after"))
baseRecalibratorAfter.BQSR = baseRecalibrator.o
add(baseRecalibratorAfter)
if (config("use_Analyze_covariates", default = false).getBoolean) {
val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after"))
baseRecalibratorAfter.BQSR = baseRecalibrator.o
add(baseRecalibratorAfter)
add(AnalyzeCovariates(this, baseRecalibrator.o, baseRecalibratorAfter.o, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
add(AnalyzeCovariates(this, baseRecalibrator.o, baseRecalibratorAfter.o, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
}
val printReads = PrintReads(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
printReads.BQSR = baseRecalibrator.o
......
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