Experiment with setting the dcov property to prevent loading of massive

shards on high coverage alignments. This should limit the number of reads loaded in a single shard to 25k
hartwigmedical · Feb 15, 2019 · c4e071a · c4e071a
1 parent c61393c
commit c4e071a
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diff --git a/QScripts/BaseRecalibration.scala b/QScripts/BaseRecalibration.scala
@@ -44,6 +44,7 @@ class BaseRecalibration extends QScript {
 
     baseRecalibrator.scatterCount = numScatters
     baseRecalibrator.nct = numCPUThreads
+    baseRecalibrator.dcov = 25000
 
     // KODU: Apply the recalibration to the sequence data
     printReads.input_file :+= bamFile

diff --git a/QScripts/IndelRealignment.scala b/QScripts/IndelRealignment.scala
@@ -48,6 +48,7 @@ class IndelRealignment extends QScript {
 				indelRealigner.targetIntervals = targetCreator.out
 				indelRealigner.input_file +:= bamFile
 				indelRealigner.scatterCount = numScatters
+        indelRealigner.dcov = 25000
 
 				indelRealigner.out = swapExt(bamFile, "bam", "realigned.bam")