Commit 8552aa61 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix on no known sites warning

parent b5ec5845
......@@ -51,7 +51,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
else if (!outputDir.endsWith("/")) outputDir += "/"
val baseRecalibrator = new BaseRecalibrator(this)
if (useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
if (preProcesBams && useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
logger.warn("No Known site found, skipping base recalibration")
useBaseRecalibration = false
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