From 08f3651d5edc46a950d8ab4c1292e124ab9bae72 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 May 2014 09:13:27 +0200
Subject: [PATCH] - Added nt and scattercount options to ApplyRecalibration
---
.../main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
index e333fb79d..db20cb677 100644
--- a/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
+++ b/gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
@@ -80,6 +80,8 @@ class Gatk(private var globalConfig: Config) extends QScript {
snpApplyRecalibration.out = swapExt(genotypeGVCFs.out,".vcf",".snp.recal.vcf")
snpApplyRecalibration.ts_filter_level = 99.5
snpApplyRecalibration.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
+ snpApplyRecalibration.nt = 3
+ snpApplyRecalibration.scatterCount = scatterCount
add(snpApplyRecalibration)
//indel recal
@@ -101,6 +103,8 @@ class Gatk(private var globalConfig: Config) extends QScript {
indelApplyRecalibration.out = swapExt(genotypeGVCFs.out,".vcf",".indel.recal.vcf")
indelApplyRecalibration.ts_filter_level = 99.0
indelApplyRecalibration.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
+ indelApplyRecalibration.nt = 3
+ indelApplyRecalibration.scatterCount = scatterCount
add(indelApplyRecalibration)
// merge snp and indels
--
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