From 6290299be3b55f1486ab7693511860f07d412465 Mon Sep 17 00:00:00 2001 From: Paul Wolfe Date: Sun, 17 Feb 2019 10:54:38 -0500 Subject: [PATCH] Revert last change. Downsampling does have a positive impact on memory consumption but produces a lossy BAM, which is not acceptable. --- QScripts/BaseRecalibration.scala | 1 - QScripts/IndelRealignment.scala | 1 - 2 files changed, 2 deletions(-) diff --git a/QScripts/BaseRecalibration.scala b/QScripts/BaseRecalibration.scala index 3f38c32..81b66c1 100755 --- a/QScripts/BaseRecalibration.scala +++ b/QScripts/BaseRecalibration.scala @@ -44,7 +44,6 @@ 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 index 0fb717e..647004f 100755 --- a/QScripts/IndelRealignment.scala +++ b/QScripts/IndelRealignment.scala @@ -48,7 +48,6 @@ 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")