diff --git a/Sarek-data b/Sarek-data
index d717855502..ba299d76c8 160000
--- a/Sarek-data
+++ b/Sarek-data
@@ -1 +1 @@
-Subproject commit d717855502f2e7501e124f2fe116733fc01ae114
+Subproject commit ba299d76c851dc916c051ef5f77d7a4ab39dcc9f
diff --git a/annotate.nf b/annotate.nf
index c1e085f633..d3571a15cd 100644
--- a/annotate.nf
+++ b/annotate.nf
@@ -73,23 +73,23 @@ vcfToAnnotate = Channel.create()
 vcfNotToAnnotate = Channel.create()
 
 if (annotateVCF == []) {
+// we annote all available vcfs by default that we can find in the VariantCalling directory
   Channel.empty().mix(
     Channel.fromPath("${directoryMap.haplotypecaller}/*.vcf.gz")
       .flatten().map{vcf -> ['haplotypecaller', vcf]},
     Channel.fromPath("${directoryMap.manta}/*SV.vcf.gz")
       .flatten().map{vcf -> ['manta', vcf]},
-    Channel.fromPath("${directoryMap.mutect1}/*.vcf.gz")
-      .flatten().map{vcf -> ['mutect1', vcf]},
     Channel.fromPath("${directoryMap.mutect2}/*.vcf.gz")
       .flatten().map{vcf -> ['mutect2', vcf]},
-    Channel.fromPath("${directoryMap.strelka}/*{somatic,variants}*.vcf.gz")
+    Channel.fromPath("${directoryMap.strelka}/*{somatic,variants}*.vcf.gz")		// Strelka only
       .flatten().map{vcf -> ['strelka', vcf]},
-    Channel.fromPath("${directoryMap.strelkabp}/*{somatic,variants}*.vcf.gz")
+    Channel.fromPath("${directoryMap.strelkabp}/*{somatic,variants}*.vcf.gz")	// Strelka with Manta indel candidates
       .flatten().map{vcf -> ['strelkabp', vcf]}
   ).choice(vcfToAnnotate, vcfNotToAnnotate) {
     annotateTools == [] || (annotateTools != [] && it[0] in annotateTools) ? 0 : 1
   }
 } else if (annotateTools == []) {
+// alternatively, annotate user-submitted VCFs
   list = ""
   annotateVCF.each{ list += ",${it}" }
   list = list.substring(1)
@@ -101,6 +101,10 @@ if (annotateVCF == []) {
 
 vcfNotToAnnotate.close()
 
+// as now have the list of VCFs to annotate, the first step is to annotate with allele frequencies, if there are any
+
+
+
 (vcfForBCFtools, vcfForVCFtools, vcfForSnpeff, vcfForVep) = vcfToAnnotate.into(4)
 
 vcfForVep = vcfForVep.map {
@@ -224,11 +228,12 @@ process RunVEP {
   finalannotator = annotator == "snpeff" ? 'merge' : 'vep'
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
   """
-  vep \
+  vep --dir /opt/vep/.vep/ \
   -i ${vcf} \
   -o ${vcf.simpleName}_VEP.ann.vcf \
   --assembly ${genome} \
   --cache \
+	--cache_version 91 \
   --database \
   --everything \
   --filter_common \
@@ -346,7 +351,6 @@ def helpMessage() {
   log.info "       Possible values are:"
   log.info "         haplotypecaller (Annotate HaplotypeCaller output)"
   log.info "         manta (Annotate Manta output)"
-  log.info "         mutect1 (Annotate MuTect1 output)"
   log.info "         mutect2 (Annotate MuTect2 output)"
   log.info "         strelka (Annotate Strelka output)"
   log.info "    --annotateVCF"
diff --git a/buildContainers.nf b/buildContainers.nf
index ba6d96ff32..92294ff432 100644
--- a/buildContainers.nf
+++ b/buildContainers.nf
@@ -177,13 +177,6 @@ def grabRevision() {
 def defineContainersList(){
   // Return list of authorized containers
   return [
-    'freebayes',
-    'gatk',
-    'gatk4',
-    'igvtools',
-    'mutect1',
-    'picard',
-    'qctools',
     'r-base',
     'runallelecount',
     'sarek',
@@ -208,8 +201,7 @@ def helpMessage() {
   log.info "    --containers: Choose which containers to build"
   log.info "       Default: all"
   log.info "       Possible values:"
-  log.info "         all, freebayes, gatk, gatk4, igvtools, mutect1, picard"
-  log.info "         qctools, r-base, runallelecount, sarek, snpeff"
+  log.info "         all, r-base, runallelecount, sarek, snpeff"
   log.info "         snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
   log.info "    --docker: Build containers using Docker"
   log.info "    --help"
diff --git a/buildReferences.nf b/buildReferences.nf
index eb185ce271..cfc7a567a2 100644
--- a/buildReferences.nf
+++ b/buildReferences.nf
@@ -29,7 +29,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - ProcessReference - Download all references if needed
  - DecompressFile - Extract files if needed
  - BuildBWAindexes - Build indexes for BWA
- - BuildPicardIndex - Build index with Picard
+ - BuildReferenceIndex - Build index for FASTA refs
  - BuildSAMToolsIndex - Build index with SAMTools
  - BuildVCFIndex - Build index for VCF files
 ================================================================================
@@ -98,7 +98,7 @@ if (params.verbose) ch_decompressedFiles = ch_decompressedFiles.view {
 
 ch_fastaFile = Channel.create()
 ch_fastaForBWA = Channel.create()
-ch_fastaForPicard = Channel.create()
+ch_fastaReference = Channel.create()
 ch_fastaForSAMTools = Channel.create()
 ch_otherFile = Channel.create()
 ch_vcfFile = Channel.create()
@@ -108,7 +108,7 @@ ch_decompressedFiles
     it =~ ".fasta" ? 0 :
     it =~ ".vcf" ? 1 : 2}
 
-(ch_fastaForBWA, ch_fastaForPicard, ch_fastaForSAMTools, ch_fastaFileToKeep) = ch_fastaFile.into(4)
+(ch_fastaForBWA, ch_fastaReference, ch_fastaForSAMTools, ch_fastaFileToKeep) = ch_fastaFile.into(4)
 (ch_vcfFile, ch_vcfFileToKeep) = ch_vcfFile.into(2)
 
 ch_notCompressedfiles
@@ -137,29 +137,28 @@ if (params.verbose) bwaIndexes.flatten().view {
   "BWA index           : ${it.fileName}"
 }
 
-process BuildPicardIndex {
+process BuildReferenceIndex {
   tag {f_reference}
 
   publishDir params.outDir, mode: 'link'
 
   input:
-    file(f_reference) from ch_fastaForPicard
+    file(f_reference) from ch_fastaReference
 
   output:
-    file("*.dict") into ch_picardIndex
+    file("*.dict") into ch_referenceIndex
 
   script:
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$PICARD_HOME/picard.jar \
+  gatk --java-options "-Xmx${task.memory.toGiga()}g" \
   CreateSequenceDictionary \
-  REFERENCE=${f_reference} \
-  OUTPUT=${f_reference.baseName}.dict
+  --REFERENCE ${f_reference} \
+  --OUTPUT ${f_reference.baseName}.dict
   """
 }
 
-if (params.verbose) ch_picardIndex.view {
-  "Picard index        : ${it.fileName}"
+if (params.verbose) ch_referenceIndex.view {
+  "Reference index        : ${it.fileName}"
 }
 
 process BuildSAMToolsIndex {
@@ -196,7 +195,7 @@ process BuildVCFIndex {
 
   script:
   """
-  \$IGVTOOLS_HOME/igvtools index ${f_reference}
+  igvtools index ${f_reference}
   """
 }
 
diff --git a/configuration/containers.config b/configuration/containers.config
index 07b862c441..5639a291fa 100644
--- a/configuration/containers.config
+++ b/configuration/containers.config
@@ -9,52 +9,48 @@
 
 process {
   $BuildBWAindexes.container          = "${params.repository}/sarek:${params.tag}"
-  $BuildPicardIndex.container         = "${params.repository}/picard:${params.tag}"
+  $BuildReferenceIndex.container         = "${params.repository}/sarek:${params.tag}"
   $BuildSAMToolsIndex.container       = "${params.repository}/sarek:${params.tag}"
-  $BuildVCFIndex.container            = "${params.repository}/igvtools:${params.tag}"
+  $BuildVCFIndex.container            = "${params.repository}/sarek:${params.tag}"
   $CompressVCF.container              = "${params.repository}/sarek:${params.tag}"
   $ConcatVCF.container                = "${params.repository}/sarek:${params.tag}"
-  $CreateRecalibrationTable.container = "${params.repository}/gatk:${params.tag}"
-  $GetVersionAll.container            = "${params.repository}/qctools:${params.tag}"
+  $CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}"
+  $GetVersionAll.container            = "${params.repository}/sarek:${params.tag}"
   $GetVersionAlleleCount.container    = "${params.repository}/runallelecount:${params.tag}"
   $GetVersionASCAT.container          = "${params.repository}/r-base:${params.tag}"
-  $GetVersionBamQC.container          = "${params.repository}/qctools:${params.tag}"
+  $GetVersionBamQC.container          = "${params.repository}/sarek:${params.tag}"
   $GetVersionBCFtools.container       = "${params.repository}/sarek:${params.tag}"
   $GetVersionBWAsamtools.container    = "${params.repository}/sarek:${params.tag}"
-  $GetVersionFastQC.container         = "${params.repository}/qctools:${params.tag}"
-  $GetVersionFreeBayes.container      = "${params.repository}/freebayes:${params.tag}"
-  $GetVersionGATK.container           = "${params.repository}/gatk:${params.tag}"
+  $GetVersionFastQC.container         = "${params.repository}/sarek:${params.tag}"
+  $GetVersionFreeBayes.container      = "${params.repository}/sarek:${params.tag}"
+  $GetVersionGATK.container           = "${params.repository}/sarek:${params.tag}"
   $GetVersionManta.container          = "${params.repository}/sarek:${params.tag}"
-  $GetVersionPicard.container         = "${params.repository}/picard:${params.tag}"
   $GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
   $GetVersionStrelka.container        = "${params.repository}/sarek:${params.tag}"
-  $GetVersionVCFtools.container       = "${params.repository}/qctools:${params.tag}"
+  $GetVersionVCFtools.container       = "${params.repository}/sarek:${params.tag}"
   $GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
-  $IndelRealigner.container           = "${params.repository}/gatk:${params.tag}"
   $MapReads.container                 = "${params.repository}/sarek:${params.tag}"
-  $MarkDuplicates.container           = "${params.repository}/picard:${params.tag}"
+  $MarkDuplicates.container           = "${params.repository}/sarek:${params.tag}"
   $MergeBams.container                = "${params.repository}/sarek:${params.tag}"
-  $RealignerTargetCreator.container   = "${params.repository}/gatk:${params.tag}"
-  $RecalibrateBam.container           = "${params.repository}/gatk:${params.tag}"
+  $RecalibrateBam.container           = "${params.repository}/sarek:${params.tag}"
   $RunAlleleCount.container           = "${params.repository}/runallelecount:${params.tag}"
   $RunAscat.container                 = "${params.repository}/r-base:${params.tag}"
-  $RunBamQC.container                 = "${params.repository}/qctools:${params.tag}"
+  $RunBamQC.container                 = "${params.repository}/sarek:${params.tag}"
   $RunBcftoolsStats.container         = "${params.repository}/sarek:${params.tag}"
   $RunConvertAlleleCounts.container   = "${params.repository}/r-base:${params.tag}"
-  $RunFastQC.container                = "${params.repository}/qctools:${params.tag}"
-  $RunFreeBayes.container             = "${params.repository}/freebayes:${params.tag}"
-  $RunGenotypeGVCFs.container         = "${params.repository}/gatk:${params.tag}"
-  $RunHaplotypecaller.container       = "${params.repository}/gatk:${params.tag}"
+  $RunFastQC.container                = "${params.repository}/sarek:${params.tag}"
+  $RunFreeBayes.container             = "${params.repository}/sarek:${params.tag}"
+  $RunGenotypeGVCFs.container         = "${params.repository}/sarek:${params.tag}"
+  $RunHaplotypecaller.container       = "${params.repository}/sarek:${params.tag}"
   $RunManta.container                 = "${params.repository}/sarek:${params.tag}"
-  $RunMultiQC.container               = "${params.repository}/qctools:${params.tag}"
-  $RunMutect1.container               = "${params.repository}/mutect1:${params.tag}"
-  $RunMutect2.container               = "${params.repository}/gatk:${params.tag}"
+  $RunMultiQC.container               = "${params.repository}/sarek:${params.tag}"
+  $RunMutect2.container               = "${params.repository}/sarek:${params.tag}"
   $RunSamtoolsStats.container         = "${params.repository}/sarek:${params.tag}"
   $RunSingleManta.container           = "${params.repository}/sarek:${params.tag}"
   $RunSingleStrelka.container         = "${params.repository}/sarek:${params.tag}"
   $RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
   $RunStrelka.container               = "${params.repository}/sarek:${params.tag}"
   $RunStrelkaBP.container             = "${params.repository}/sarek:${params.tag}"
-  $RunVcftools.container              = "${params.repository}/qctools:${params.tag}"
+  $RunVcftools.container              = "${params.repository}/sarek:${params.tag}"
   $RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
 }
diff --git a/configuration/genomes.config b/configuration/genomes.config
index 56097e23fe..53ceecf9cf 100644
--- a/configuration/genomes.config
+++ b/configuration/genomes.config
@@ -42,6 +42,9 @@ params {
       knownIndels   = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       knownIndelsIndex = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
       snpeffDb      = "GRCh38.86"
+			// This a nasty-looking list of allele-frequencies files. Add/remove files to match to your sets
+			//AF_files			= "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf" 
+			//AF_indexes		= "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf.idx" 
     }
     'smallGRCh37' {
       acLoci      = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
diff --git a/configuration/singularity-path.config b/configuration/singularity-path.config
index 7efea0292f..9b51a46318 100644
--- a/configuration/singularity-path.config
+++ b/configuration/singularity-path.config
@@ -14,52 +14,50 @@ singularity {
 
 process {
   $BuildBWAindexes.container          = "${params.containerPath}/sarek-${params.tag}.img"
-  $BuildPicardIndex.container         = "${params.containerPath}/picard-${params.tag}.img"
+  $BuildReferenceIndex.container      = "${params.containerPath}/sarek-${params.tag}.img"
   $BuildSAMToolsIndex.container       = "${params.containerPath}/sarek-${params.tag}.img"
-  $BuildVCFIndex.container            = "${params.containerPath}/igvtools-${params.tag}.img"
+  $BuildVCFIndex.container            = "${params.containerPath}/sarek-${params.tag}.img"
   $CompressVCF.container              = "${params.containerPath}/sarek-${params.tag}.img"
   $ConcatVCF.container                = "${params.containerPath}/sarek-${params.tag}.img"
-  $CreateRecalibrationTable.container = "${params.containerPath}/gatk-${params.tag}.img"
-  $GetVersionAll.container            = "${params.containerPath}/qctools-${params.tag}.img"
+  $CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img"
+  $GetVersionAll.container            = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionAlleleCount.container    = "${params.containerPath}/runallelecount-${params.tag}.img"
   $GetVersionASCAT.container          = "${params.containerPath}/r-base-${params.tag}.img"
-  $GetVersionBamQC.container          = "${params.containerPath}/qctools-${params.tag}.img"
+  $GetVersionBamQC.container          = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionBCFtools.container       = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionBWAsamtools.container    = "${params.containerPath}/sarek-${params.tag}.img"
-  $GetVersionFastQC.container         = "${params.containerPath}/qctools-${params.tag}.img"
-  $GetVersionFreeBayes.container      = "${params.containerPath}/freebayes-${params.tag}.img"
-  $GetVersionGATK.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $GetVersionFastQC.container         = "${params.containerPath}/sarek-${params.tag}.img"
+  $GetVersionFreeBayes.container      = "${params.containerPath}/sarek-${params.tag}.img"
+  $GetVersionGATK.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionManta.container          = "${params.containerPath}/sarek-${params.tag}.img"
-  $GetVersionPicard.container         = "${params.containerPath}/picard-${params.tag}.img"
   $GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
   $GetVersionStrelka.container        = "${params.containerPath}/sarek-${params.tag}.img"
-  $GetVersionVCFtools.container       = "${params.containerPath}/qctools-${params.tag}.img"
+  $GetVersionVCFtools.container       = "${params.containerPath}/sarek-${params.tag}.img"
   $GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
-  $IndelRealigner.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $IndelRealigner.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $MapReads.container                 = "${params.containerPath}/sarek-${params.tag}.img"
-  $MarkDuplicates.container           = "${params.containerPath}/picard-${params.tag}.img"
+  $MarkDuplicates.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $MergeBams.container                = "${params.containerPath}/sarek-${params.tag}.img"
-  $RealignerTargetCreator.container   = "${params.containerPath}/gatk-${params.tag}.img"
-  $RecalibrateBam.container           = "${params.containerPath}/gatk-${params.tag}.img"
+  $RealignerTargetCreator.container   = "${params.containerPath}/sarek-${params.tag}.img"
+  $RecalibrateBam.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $RunAlleleCount.container           = "${params.containerPath}/runallelecount-${params.tag}.img"
   $RunAscat.container                 = "${params.containerPath}/r-base-${params.tag}.img"
-  $RunBamQC.container                 = "${params.containerPath}/qctools-${params.tag}.img"
+  $RunBamQC.container                 = "${params.containerPath}/sarek-${params.tag}.img"
   $RunBcftoolsStats.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunConvertAlleleCounts.container   = "${params.containerPath}/r-base-${params.tag}.img"
-  $RunFastQC.container                = "${params.containerPath}/qctools-${params.tag}.img"
-  $RunFreeBayes.container             = "${params.containerPath}/freebayes-${params.tag}.img"
-  $RunGenotypeGVCFs.container         = "${params.containerPath}/gatk-${params.tag}.img"
-  $RunHaplotypecaller.container       = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunFastQC.container                = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunFreeBayes.container             = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunGenotypeGVCFs.container         = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunHaplotypecaller.container       = "${params.containerPath}/sarek-${params.tag}.img"
   $RunManta.container                 = "${params.containerPath}/sarek-${params.tag}.img"
-  $RunMultiQC.container               = "${params.containerPath}/qctools-${params.tag}.img"
-  $RunMutect1.container               = "${params.containerPath}/mutect1-${params.tag}.img"
-  $RunMutect2.container               = "${params.containerPath}/gatk-${params.tag}.img"
+  $RunMultiQC.container               = "${params.containerPath}/sarek-${params.tag}.img"
+  $RunMutect2.container               = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSamtoolsStats.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSingleManta.container           = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSingleStrelka.container         = "${params.containerPath}/sarek-${params.tag}.img"
   $RunSnpeff.container                = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
   $RunStrelka.container               = "${params.containerPath}/sarek-${params.tag}.img"
   $RunStrelkaBP.container             = "${params.containerPath}/sarek-${params.tag}.img"
-  $RunVcftools.container              = "${params.containerPath}/qctools-${params.tag}.img"
+  $RunVcftools.container              = "${params.containerPath}/sarek-${params.tag}.img"
   $RunVEP.container                   = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
 }
diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
index 1f4cd5bb56..f5907f6181 100644
--- a/configuration/uppmax-localhost.config
+++ b/configuration/uppmax-localhost.config
@@ -43,7 +43,7 @@ process {
   $BuildBWAindexes {
     memory = {params.totalMemory} // TODO This is likely too high
   }
-  $BuildPicardIndex {
+  $BuildReferenceIndex {
     memory = {params.totalMemory} // TODO This is likely too high
   }
   $BuildSAMToolsIndex {
@@ -70,7 +70,9 @@ process {
     memory = {params.totalMemory}
   }
   $MarkDuplicates {
-    memory = {params.singleCPUMem * 2 * task.attempt}
+		// Actually the -Xmx value should be kept lower  
+    cpus = 16
+    memory = {2 * params.singleCPUMem}
   }
   $MergeBams {
     cpus = 16
@@ -117,10 +119,6 @@ process {
   }
   $RunMultiQC {
   }
-  $RunMutect1 {
-    cpus = 1
-    memory = {params.singleCPUMem * task.attempt}
-  }
   $RunMutect2 {
     cpus = 1
     memory = {params.singleCPUMem * task.attempt}
diff --git a/configuration/uppmax-slurm.config b/configuration/uppmax-slurm.config
index de1639964f..821a3855d8 100644
--- a/configuration/uppmax-slurm.config
+++ b/configuration/uppmax-slurm.config
@@ -27,7 +27,7 @@ process {
 
   $BuildBWAindexes {
   }
-  $BuildPicardIndex {
+  $BuildReferenceIndex {
   }
   $BuildSAMToolsIndex {
   }
@@ -52,10 +52,9 @@ process {
     time = {params.runTime * task.attempt}
   }
   $MarkDuplicates {
-    cpus = 1
-    memory = {params.singleCPUMem * 8 * task.attempt}
-    queue = 'core'
-    time = {params.runTime * task.attempt}
+		// Actually the -Xmx value should be kept lower  
+    cpus = 16
+    memory = {2 * params.singleCPUMem}
   }
   $MergeBams {
     memory = {params.singleCPUMem * task.attempt}
@@ -116,12 +115,6 @@ process {
   $RunMultiQC {
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
   }
-  $RunMutect1 {
-    queue = 'core'
-    time = {params.runTime * task.attempt}
-    cpus = 1
-    memory = {params.singleCPUMem * task.attempt}
-  }
   $RunMutect2 {
     cpus = 1
     memory = {params.singleCPUMem * task.attempt}
diff --git a/containers/freebayes/Dockerfile b/containers/freebayes/Dockerfile
deleted file mode 100644
index efacdde8ee..0000000000
--- a/containers/freebayes/Dockerfile
+++ /dev/null
@@ -1,30 +0,0 @@
-FROM debian:8.9
-
-LABEL \
-  author="Maxime Garcia" \
-  description="FreeBayes image for use in Sarek" \
-  maintainer="maxime.garcia@scilifelab.se"
-
-# Install libraries
-RUN \
-  apt-get update && apt-get install -y --no-install-recommends \
-    build-essential \
-    ca-certificates \
-    cmake \
-    git \
-    wget \
-    zlib1g-dev \
-  && rm -rf /var/lib/apt/lists/*
-
-# Setup ENV variables
-ENV FREEBAYES_VERSION=1.1.0
-
-# Install BCFTools
-RUN \
-  git clone --recursive git://github.com/ekg/freebayes.git freebayes \
-    --branch v${FREEBAYES_VERSION} \
-  && cd freebayes \
-  && make \
-  && make install \
-  && cd .. \
-&& rm -rf freebayes
diff --git a/containers/mutect1/Dockerfile b/containers/mutect1/Dockerfile
deleted file mode 100644
index 7068fb963c..0000000000
--- a/containers/mutect1/Dockerfile
+++ /dev/null
@@ -1,25 +0,0 @@
-FROM openjdk:7-slim
-
-LABEL \
-  author="Maxime Garcia" \
-  description="MuTect 1.1.5 image for use in Sarek" \
-  maintainer="maxime.garcia@scilifelab.se"
-
-# Install libraries
-RUN \
-  apt-get update && apt-get install -y --no-install-recommends \
-    wget \
-  && rm -rf /var/lib/apt/lists/*
-
-# Setup ENV variables
-ENV \
-  MUTECT_HOME=/opt/mutect-1.1.5 \
-  MUTECT_VERSION=1.1.5
-
-# Install MuTect1
-RUN \
-  wget --quiet -O muTect-${MUTECT_VERSION}-bin.zip \
-    https://github.com/broadinstitute/mutect/releases/download/${MUTECT_VERSION}/muTect-${MUTECT_VERSION}-bin.zip \
-  && unzip muTect-${MUTECT_VERSION}-bin.zip -d ${MUTECT_HOME} \
-  && rm muTect-${MUTECT_VERSION}-bin.zip \
-&& mv ${MUTECT_HOME}/muTect-${MUTECT_VERSION}.jar ${MUTECT_HOME}/muTect.jar
diff --git a/containers/sarek/Dockerfile b/containers/sarek/Dockerfile
index 7ef82bbd8a..340e699e71 100644
--- a/containers/sarek/Dockerfile
+++ b/containers/sarek/Dockerfile
@@ -1,18 +1,10 @@
-FROM debian:8.9
+FROM nfcore/base:latest
 
 LABEL \
-  author="Maxime Garcia" \
+  authors="Maxime.Garcia@scilifelab.se, Szilveszter.Juhos@scilifelab.se" \
   description="Image with tools used in Sarek" \
-  maintainer="maxime.garcia@scilifelab.se"
+	maintainer="Maxime Garcia <maxime.garcia@scilifelab.se>, Szilveszter Juhos <Szilveszter.Juhos@scilifelab.se>"
 
-# Export PATH
-ENV \
-  MANTA_INSTALL_PATH=/opt/manta \
-  PATH=/opt/bcftools/bin:/opt/htslib/bin:/opt/samtools/bin:$PATH \
-  STRELKA_INSTALL_PATH=/opt/strelka
-
-# Build container
-ADD \
-  build.sh /usr/bin/
-RUN \
-  build.sh
+COPY environment.yml /
+RUN conda env update -n root -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/bin:$PATH
diff --git a/containers/sarek/build.sh b/containers/sarek/build.sh
deleted file mode 100755
index fbe57b5aee..0000000000
--- a/containers/sarek/build.sh
+++ /dev/null
@@ -1,103 +0,0 @@
-#!/bin/sh
-set -eu pipefail
-
-# Local ENV variables
-BCFTOOLS_VERSION=1.5
-BWA_VERSION=0.7.16
-HTSLIB_VERSION=1.5
-MANTA_VERSION=1.1.1
-SAMTOOLS_VERSION=1.5
-STRELKA_VERSION=2.8.2
-
-# Install libraries
-apt-get update && apt-get install -y --no-install-recommends \
-  build-essential \
-  bzip2 \
-  ca-certificates \
-  g++ \
-  gcc \
-  git \
-  libbz2-dev \
-  liblzma-dev \
-  libncurses5-dev \
-  libncursesw5-dev \
-  make \
-  python \
-  python3 \
-  unzip \
-  wget \
-  zlib1g-dev
-
-# Install tools
-mkdir /build
-
-# Install BWA
-cd /build
-git clone http://github.com/lh3/bwa.git bwa \
-  --branch v${BWA_VERSION}
-cd bwa
-make
-cp bwa /usr/local/bin/bwa
-
-# Install HTSlib
-cd /build
-wget --quiet -O htslib-${HTSLIB_VERSION}.tar.bz2 \
-  https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
-tar xfj htslib-${HTSLIB_VERSION}.tar.bz2
-rm htslib-${HTSLIB_VERSION}.tar.bz2
-cd htslib-${HTSLIB_VERSION}
-./configure --prefix=/opt/htslib
-make && make install
-
-# Install BCFtools
-cd /build
-wget --quiet -O bcftools-${BCFTOOLS_VERSION}.tar.bz2 \
-  https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
-tar xfj bcftools-${BCFTOOLS_VERSION}.tar.bz2
-rm bcftools-${BCFTOOLS_VERSION}.tar.bz2
-cd bcftools-${BCFTOOLS_VERSION}
-./configure --prefix=/opt/bcftools
-make && make install
-
-# Install Samtools
-cd /build
-wget --quiet -O samtools-${SAMTOOLS_VERSION}.tar.bz2 \
-  https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2
-tar xfj samtools-${SAMTOOLS_VERSION}.tar.bz2
-rm samtools-${SAMTOOLS_VERSION}.tar.bz2
-cd samtools-${SAMTOOLS_VERSION}
-./configure --prefix=/opt/samtools
-make && make install
-
-# Install Manta
-cd /build
-wget --quiet -O manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2 \
-  https://github.com/Illumina/manta/releases/download/v${MANTA_VERSION}/manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2
-tar xvjf manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2
-mv manta-${MANTA_VERSION}.centos5_x86_64 $MANTA_INSTALL_PATH
-rm manta-${MANTA_VERSION}.centos5_x86_64.tar.bz2
-
-# Install Strelka
-cd /build
-wget --quiet -O strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2 \
-  https://github.com/Illumina/strelka/releases/download/v${STRELKA_VERSION}/strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2
-tar xvjf strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2
-mv strelka-${STRELKA_VERSION}.centos5_x86_64 $STRELKA_INSTALL_PATH
-rm strelka-${STRELKA_VERSION}.centos5_x86_64.tar.bz2
-
-# Clean up install
-cd /
-apt-get remove -y \
-  build-essential \
-  ca-certificates \
-  gcc \
-  git \
-  libbz2-dev \
-  liblzma-dev \
-  libncurses5-dev \
-  libncursesw5-dev \
-  unzip \
-  wget \
-  zlib1g-dev
-apt-get clean
-rm -rf /build /var/lib/apt/lists/* /opt/get-pip.py
diff --git a/containers/sarek/environment.yml b/containers/sarek/environment.yml
new file mode 100644
index 0000000000..af3ea825f4
--- /dev/null
+++ b/containers/sarek/environment.yml
@@ -0,0 +1,24 @@
+# You can use this file to create a conda environment for this pipeline:
+# conda env create -f environment.yml
+name: sarek
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+
+dependencies:
+  - bcftools=1.8
+  - bwa=0.7.17
+  - conda-forge::openjdk=8.0.144 # Needed for FastQC docker - see bioconda/bioconda-recipes#5026
+  - fastqc=0.11.7
+  - freebayes=1.2.0
+  - gatk4=4.0.6.0
+  - htslib=1.9
+  - igvtools=2.3.93
+  - manta=1.4.0
+  - multiqc=1.5
+  - qualimap=2.2.2a
+  - samtools=1.8
+  - strelka=2.9.3
+  - vcfanno=0.2.8
+  - vcftools=0.1.15
diff --git a/doc/images/GitHub.QR.png b/doc/images/GitHub.QR.png
new file mode 100644
index 0000000000..f20bee47fa
Binary files /dev/null and b/doc/images/GitHub.QR.png differ
diff --git a/germlineVC.nf b/germlineVC.nf
index ea3ab75700..4dd71fb528 100644
--- a/germlineVC.nf
+++ b/germlineVC.nf
@@ -31,7 +31,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - CreateIntervalBeds - Create and sort intervals into bed files
  - RunHaplotypecaller - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
  - RunGenotypeGVCFs - Run HaplotypeCaller for Germline Variant Calling (Parallelized processes)
- - ConcatVCF - Merge results from HaplotypeCaller, MuTect1 and MuTect2
+ - ConcatVCF - Merge results from HaplotypeCaller, MuTect2 and other paralellized callers
  - RunSingleStrelka - Run Strelka for Germline Variant Calling
  - RunSingleManta - Run Manta for Single Structural Variant Calling
  - RunBcftoolsStats - Run BCFTools stats on vcf files
@@ -71,9 +71,6 @@ if (params.test && params.genome in ['GRCh37', 'GRCh38']) {
   referenceMap.intervals = file("$workflow.projectDir/repeats/tiny_${params.genome}.list")
 }
 
-// TODO
-// MuTect and Mutect2 could be run without a recalibrated BAM (they support
-// the --BQSR option), but this is not implemented, yet.
 // TODO
 // FreeBayes does not need recalibrated BAMs, but we need to test whether
 // the channels are set up correctly when we disable it
@@ -287,8 +284,8 @@ bamsAll = bamsAll.map {
 
 bamsTumorNormalIntervals = bamsAll.spread(bedIntervals)
 
-// MuTect1, MuTect2, FreeBayes
-(bamsFMT1, bamsFMT2, bamsFFB) = bamsTumorNormalIntervals.into(3)
+// MuTect2, FreeBayes
+(bamsFMT2, bamsFFB) = bamsTumorNormalIntervals.into(2)
 
 process RunHaplotypecaller {
   tag {idSample + "-" + intervalBed.baseName}
@@ -310,20 +307,15 @@ process RunHaplotypecaller {
   when: 'haplotypecaller' in tools && !params.onlyQC
 
   script:
-  BQSR = (recalTable != null) ? "--BQSR $recalTable" : ''
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T HaplotypeCaller \
-  --emitRefConfidence GVCF \
-  -pairHMM LOGLESS_CACHING \
-  -R ${genomeFile} \
-  --dbsnp ${dbsnp} \
-  ${BQSR} \
-  -I ${bam} \
-  -L ${intervalBed} \
-  --disable_auto_index_creation_and_locking_when_reading_rods \
-  -o ${intervalBed.baseName}_${idSample}.g.vcf
+  gatk --java-options "-Xmx${task.memory.toGiga()}g -Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
+      HaplotypeCaller \
+      -R ${genomeFile} \
+      -I ${bam} \
+      -L ${intervalBed} \
+      --dbsnp ${dbsnp} \
+      -O ${intervalBed.baseName}_${idSample}.g.vcf \
+      --emit-ref-confidence GVCF
   """
 }
 hcGenomicVCF = hcGenomicVCF.groupTuple(by:[0,1,2,3])
@@ -349,17 +341,17 @@ process RunGenotypeGVCFs {
   when: 'haplotypecaller' in tools && !params.onlyQC
 
   script:
-  // Using -L is important for speed
+  // Using -L is important for speed and we have to index the interval files also
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T GenotypeGVCFs \
+  gatk IndexFeatureFile -F ${gvcf}
+
+  gatk --java-options -Xmx${task.memory.toGiga()}g \
+  GenotypeGVCFs \
   -R ${genomeFile} \
   -L ${intervalBed} \
   --dbsnp ${dbsnp} \
-  --variant ${gvcf} \
-  --disable_auto_index_creation_and_locking_when_reading_rods \
-  -o ${intervalBed.baseName}_${idSample}.vcf
+  -V ${gvcf} \
+  -O ${intervalBed.baseName}_${idSample}.vcf
   """
 }
 hcGenotypedVCF = hcGenotypedVCF.groupTuple(by:[0,1,2,3])
@@ -387,7 +379,7 @@ process ConcatVCF {
     set variantCaller, idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into vcfConcatenated
 
 
-  when: ( 'haplotypecaller' in tools || 'mutect1' in tools || 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC
+  when: ( 'haplotypecaller' in tools || 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC
 
   script:
   if (variantCaller == 'haplotypecaller') outputFile = "${variantCaller}_${idSampleNormal}.vcf"
@@ -395,6 +387,7 @@ process ConcatVCF {
   else outputFile = "${variantCaller}_${idSampleTumor}_vs_${idSampleNormal}.vcf"
 
   """
+	set -euo pipefail
   # first make a header from one of the VCF intervals
   # get rid of interval information only from the GATK command-line, but leave the rest
   FIRSTVCF=\$(ls *.vcf | head -n 1)
@@ -462,7 +455,7 @@ process RunSingleStrelka {
 
   script:
   """
-  \$STRELKA_INSTALL_PATH/bin/configureStrelkaGermlineWorkflow.py \
+  configureStrelkaGermlineWorkflow.py \
   --bam ${bam} \
   --referenceFasta ${genomeFile} \
   --runDir Strelka
@@ -506,7 +499,7 @@ process RunSingleManta {
 
   script:
   """
-  \$MANTA_INSTALL_PATH/bin/configManta.py \
+  configManta.py \
   --bam ${bam} \
   --reference ${genomeFile} \
   --runDir Manta
@@ -670,7 +663,6 @@ def defineToolList() {
     'freebayes',
     'haplotypecaller',
     'manta',
-    'mutect1',
     'mutect2',
     'strelka'
   ]
diff --git a/lib/QC.groovy b/lib/QC.groovy
index 2b228a8b68..2f6885d84b 100644
--- a/lib/QC.groovy
+++ b/lib/QC.groovy
@@ -59,14 +59,14 @@ class QC {
 // Get GATK version
   static def getVersionGATK() {
     """
-    echo "GATK version"\$(java -jar \$GATK_HOME/GenomeAnalysisTK.jar --version 2>&1) > v_gatk.txt
+		gatk ApplyBQSR --help 2>&1| awk -F/ '/java/{for(i=1;i<=NF;i++){if(\$i~/gatk4/){sub("gatk4-","",\$i);print \$i>"v_gatk.txt"}}}'
     """
   }
 
 // Get Manta version
   static def getVersionManta() {
     """
-    cat \$MANTA_INSTALL_PATH/lib/python/configBuildTimeInfo.py | grep workflowVersion > v_manta.txt
+		configManta.py --version > v_manta.txt
     """
   }
 
@@ -80,7 +80,7 @@ class QC {
 // Get Strelka version
   static def getVersionStrelka() {
     """
-    cat \$STRELKA_INSTALL_PATH/lib/python/configBuildTimeInfo.py | grep workflowVersion > v_strelka.txt
+		configureStrelkaGermlineWorkflow.py --version > v_strelka.txt
     """
   }
 
diff --git a/lib/SarekUtils.groovy b/lib/SarekUtils.groovy
index 2a95d198b1..43287f0388 100644
--- a/lib/SarekUtils.groovy
+++ b/lib/SarekUtils.groovy
@@ -100,13 +100,14 @@ class SarekUtils {
   }
 
   // Loop through all the references files to check their existence
+
   static def checkRefExistence(referenceFile, fileToCheck) {
     if (fileToCheck instanceof List) return fileToCheck.every{ SarekUtils.checkRefExistence(referenceFile, it) }
     def f = file(fileToCheck)
     // this is an expanded wildcard: we can assume all files exist
     if (f instanceof List && f.size() > 0) return true
-    else if (!f.exists()) {
-      this.log.info  "Missing references: ${referenceFile} ${fileToCheck}"
+    else if (!f.exists()) { 
+			println  "Missing references: ${referenceFile} ${fileToCheck}"
       return false
     }
     return true
@@ -115,15 +116,13 @@ class SarekUtils {
   // Define map of directories
   static def defineDirectoryMap(outDir) {
     return [
-    'nonRealigned'     : "${outDir}/Preprocessing/NonRealigned",
-    'nonRecalibrated'  : "${outDir}/Preprocessing/NonRecalibrated",
+    'duplicateMarked'  : "${outDir}/Preprocessing/DuplicateMarked",
     'recalibrated'     : "${outDir}/Preprocessing/Recalibrated",
     'ascat'            : "${outDir}/VariantCalling/Ascat",
     'freebayes'        : "${outDir}/VariantCalling/FreeBayes",
     'gvcf-hc'          : "${outDir}/VariantCalling/HaplotypeCallerGVCF",
     'haplotypecaller'  : "${outDir}/VariantCalling/HaplotypeCaller",
     'manta'            : "${outDir}/VariantCalling/Manta",
-    'mutect1'          : "${outDir}/VariantCalling/MuTect1",
     'mutect2'          : "${outDir}/VariantCalling/MuTect2",
     'strelka'          : "${outDir}/VariantCalling/Strelka",
     'strelkabp'        : "${outDir}/VariantCalling/StrelkaBP",
diff --git a/main.nf b/main.nf
index f683d397b6..ecd26d3461 100644
--- a/main.nf
+++ b/main.nf
@@ -29,8 +29,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - RunFastQC - Run FastQC for QC on fastq files
  - MapReads - Map reads with BWA
  - MergeBams - Merge BAMs if multilane samples
- - MarkDuplicates - Mark Duplicates with Picard
- - RealignerTargetCreator - Create realignment target intervals
+ - MarkDuplicates - Mark Duplicates with GATK4
  - IndelRealigner - Realign BAMs as T/N pair
  - CreateRecalibrationTable - Create Recalibration Table with BaseRecalibrator
  - RecalibrateBam - Recalibrate Bam with PrintReads
@@ -83,8 +82,7 @@ if (params.sample) tsvPath = params.sample
 if (!params.sample && !params.sampleDir) {
   tsvPaths = [
       'mapping': "${workflow.projectDir}/Sarek-data/testdata/tsv/tiny.tsv",
-      'realign': "${directoryMap.nonRealigned}/nonRealigned.tsv",
-      'recalibrate': "${directoryMap.nonRecalibrated}/nonRecalibrated.tsv"
+      'recalibrate': "${directoryMap.duplicateMarked}/duplicateMarked.tsv"
   ]
   if (params.test || step != 'mapping') tsvPath = tsvPaths[step]
 }
@@ -97,7 +95,6 @@ if (tsvPath) {
   tsvFile = file(tsvPath)
   switch (step) {
     case 'mapping': fastqFiles = extractFastq(tsvFile); break
-    case 'realign': bamFiles = SarekUtils.extractBams(tsvFile, "somatic"); break
     case 'recalibrate': bamFiles = extractRecal(tsvFile); break
     default: exit 1, "Unknown step ${step}"
   }
@@ -182,7 +179,7 @@ process MapReads {
   """
   bwa mem -R \"${readGroup}\" ${extra} -t ${task.cpus} -M \
   ${genomeFile} ${fastqFile1} ${fastqFile2} | \
-  samtools sort --threads ${task.cpus} -m 4G - > ${idRun}.bam
+  samtools sort --threads ${task.cpus} -m 2G - > ${idRun}.bam
   """
 }
 
@@ -247,14 +244,14 @@ process MarkDuplicates {
   publishDir params.outDir, mode: 'link',
     saveAs: {
       if (it == "${bam}.metrics") "${directoryMap.markDuplicatesQC}/${it}"
-      else "${directoryMap.nonRealigned}/${it}"
+      else "${directoryMap.duplicateMarked}/${it}"
     }
 
   input:
     set idPatient, status, idSample, file(bam) from mergedBam
 
   output:
-    set idPatient, file("${idSample}_${status}.md.bam"), file("${idSample}_${status}.md.bai") into duplicates
+    set idPatient, file("${idSample}_${status}.md.bam"), file("${idSample}_${status}.md.bai") into duplicateMarkedBams
     set idPatient, status, idSample, val("${idSample}_${status}.md.bam"), val("${idSample}_${status}.md.bai") into markDuplicatesTSV
     file ("${bam}.metrics") into markDuplicatesReport
 
@@ -262,150 +259,27 @@ process MarkDuplicates {
 
   script:
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$PICARD_HOME/picard.jar MarkDuplicates \
-  INPUT=${bam} \
-  METRICS_FILE=${bam}.metrics \
-  TMP_DIR=. \
-  ASSUME_SORTED=true \
-  VALIDATION_STRINGENCY=LENIENT \
-  CREATE_INDEX=TRUE \
-  OUTPUT=${idSample}_${status}.md.bam
+  gatk --java-options -Xmx${task.memory.toGiga()}g \
+  MarkDuplicates \
+  --MAX_RECORDS_IN_RAM 50000 \
+  --INPUT ${bam} \
+  --METRICS_FILE ${bam}.metrics \
+  --TMP_DIR . \
+  --ASSUME_SORT_ORDER coordinate \
+  --CREATE_INDEX true \
+  --OUTPUT ${idSample}_${status}.md.bam
   """
 }
 
 // Creating a TSV file to restart from this step
 markDuplicatesTSV.map { idPatient, status, idSample, bam, bai ->
   gender = patientGenders[idPatient]
-  "${idPatient}\t${gender}\t${status}\t${idSample}\t${directoryMap.nonRealigned}/${bam}\t${directoryMap.nonRealigned}/${bai}\n"
+  "${idPatient}\t${gender}\t${status}\t${idSample}\t${directoryMap.duplicateMarked}/${bam}\t${directoryMap.duplicateMarked}/${bai}\n"
 }.collectFile(
-  name: 'nonRealigned.tsv', sort: true, storeDir: directoryMap.nonRealigned
+  name: 'duplicateMarked.tsv', sort: true, storeDir: directoryMap.duplicateMarked
 )
 
-// Create intervals for realignement using both tumor+normal as input
-// Group the marked duplicates BAMs for intervals and realign by idPatient
-// Grouping also by gender, to make a nicer channel
-duplicatesGrouped = Channel.empty()
-if (step == 'mapping') duplicatesGrouped = duplicates.groupTuple()
-else if (step == 'realign') duplicatesGrouped = bamFiles.map{
-  idPatient, status, idSample, bam, bai ->
-  [idPatient, bam, bai]
-}.groupTuple()
-
-// The duplicatesGrouped channel is duplicated
-// one copy goes to the RealignerTargetCreator process
-// and the other to the IndelRealigner process
-(duplicatesInterval, duplicatesRealign) = duplicatesGrouped.into(2)
-
-if (params.verbose) duplicatesInterval = duplicatesInterval.view {
-  "BAMs for RealignerTargetCreator:\n\
-  ID    : ${it[0]}\n\
-  Files : ${it[1].fileName}\n\
-  Files : ${it[2].fileName}"
-}
-
-if (params.verbose) duplicatesRealign = duplicatesRealign.view {
-  "BAMs to join:\n\
-  ID    : ${it[0]}\n\
-  Files : ${it[1].fileName}\n\
-  Files : ${it[2].fileName}"
-}
-
-if (params.verbose) markDuplicatesReport = markDuplicatesReport.view {
-  "MarkDuplicates report:\n\
-  File  : [${it.fileName}]"
-}
-
-// VCF indexes are added so they will be linked, and not re-created on the fly
-//  -L "1:131941-141339" \
-
-process RealignerTargetCreator {
-  tag {idPatient}
-
-  input:
-    set idPatient, file(bam), file(bai) from duplicatesInterval
-    set file(genomeFile), file(genomeIndex), file(genomeDict), file(knownIndels), file(knownIndelsIndex), file(intervals) from Channel.value([
-      referenceMap.genomeFile,
-      referenceMap.genomeIndex,
-      referenceMap.genomeDict,
-      referenceMap.knownIndels,
-      referenceMap.knownIndelsIndex,
-      referenceMap.intervals
-    ])
-
-  output:
-    set idPatient, file("${idPatient}.intervals") into intervals
-
-  when: ( step == 'mapping' || step == 'realign' ) && !params.onlyQC
-
-  script:
-  bams = bam.collect{"-I ${it}"}.join(' ')
-  known = knownIndels.collect{"-known ${it}"}.join(' ')
-  """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T RealignerTargetCreator \
-  ${bams} \
-  -R ${genomeFile} \
-  ${known} \
-  -nt ${task.cpus} \
-  -L ${intervals} \
-  -o ${idPatient}.intervals
-  """
-}
-
-if (params.verbose) intervals = intervals.view {
-  "Intervals to join:\n\
-  ID    : ${it[0]}\n\
-  File  : [${it[1].fileName}]"
-}
-
-bamsAndIntervals = duplicatesRealign.join(intervals)
-
-if (params.verbose) bamsAndIntervals = bamsAndIntervals.view {
-  "BAMs and Intervals joined for IndelRealigner:\n\
-  ID    : ${it[0]}\n\
-  Files : ${it[1].fileName}\n\
-  Files : ${it[2].fileName}\n\
-  File  : [${it[3].fileName}]"
-}
-
-// use nWayOut to split into T/N pair again
-process IndelRealigner {
-  tag {idPatient}
-
-  publishDir directoryMap.nonRecalibrated, mode: 'link'
-
-  input:
-    set idPatient, file(bam), file(bai), file(intervals) from bamsAndIntervals
-    set file(genomeFile), file(genomeIndex), file(genomeDict), file(knownIndels), file(knownIndelsIndex) from Channel.value([
-      referenceMap.genomeFile,
-      referenceMap.genomeIndex,
-      referenceMap.genomeDict,
-      referenceMap.knownIndels,
-      referenceMap.knownIndelsIndex])
-
-  output:
-    set idPatient, file("*.real.bam"), file("*.real.bai") into realignedBam mode flatten
-
-  when: ( step == 'mapping' || step == 'realign' ) && !params.onlyQC
-
-  script:
-  bams = bam.collect{"-I ${it}"}.join(' ')
-  known = knownIndels.collect{"-known ${it}"}.join(' ')
-  """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T IndelRealigner \
-  ${bams} \
-  -R ${genomeFile} \
-  -targetIntervals ${intervals} \
-  ${known} \
-  -nWayOut '.real.bam'
-  """
-}
-
-realignedBam = realignedBam.map {
+duplicateMarkedBams = duplicateMarkedBams.map {
     idPatient, bam, bai ->
     tag = bam.baseName.tokenize('.')[0]
     status   = tag[-1..-1].toInteger()
@@ -413,21 +287,21 @@ realignedBam = realignedBam.map {
     [idPatient, status, idSample, bam, bai]
 }
 
-if (params.verbose) realignedBam = realignedBam.view {
+if (params.verbose) duplicateMarkedBams = duplicateMarkedBams.view {
   "Realigned BAM to CreateRecalibrationTable:\n\
   ID    : ${it[0]}\tStatus: ${it[1]}\tSample: ${it[2]}\n\
   Files : [${it[3].fileName}, ${it[4].fileName}]"
 }
 
-(realignedBam, realignedBamToJoin) = realignedBam.into(2)
+(mdBam, mdBamToJoin) = duplicateMarkedBams.into(2)
 
 process CreateRecalibrationTable {
   tag {idPatient + "-" + idSample}
 
-  publishDir directoryMap.nonRecalibrated, mode: 'link', overwrite: false
+  publishDir directoryMap.duplicateMarked, mode: 'link', overwrite: false
 
   input:
-    set idPatient, status, idSample, file(bam), file(bai) from realignedBam
+    set idPatient, status, idSample, file(bam), file(bai) from mdBam // realignedBam
     set file(genomeFile), file(genomeIndex), file(genomeDict), file(dbsnp), file(dbsnpIndex), file(knownIndels), file(knownIndelsIndex), file(intervals) from Channel.value([
       referenceMap.genomeFile,
       referenceMap.genomeIndex,
@@ -441,37 +315,35 @@ process CreateRecalibrationTable {
 
   output:
     set idPatient, status, idSample, file("${idSample}.recal.table") into recalibrationTable
-    set idPatient, status, idSample, val("${idSample}_${status}.md.real.bam"), val("${idSample}_${status}.md.real.bai"), val("${idSample}.recal.table") into recalibrationTableTSV
+    set idPatient, status, idSample, val("${idSample}_${status}.md.bam"), val("${idSample}_${status}.md.bai"), val("${idSample}.recal.table") into recalibrationTableTSV
 
-  when: ( step == 'mapping' || step == 'realign' ) && !params.onlyQC
+  when: ( step == 'mapping' ) && !params.onlyQC
 
   script:
-  known = knownIndels.collect{ "-knownSites ${it}" }.join(' ')
+  known = knownIndels.collect{ "--known-sites ${it}" }.join(' ')
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -Djava.io.tmpdir="/tmp" \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T BaseRecalibrator \
+  gatk --java-options -Xmx${task.memory.toGiga()}g \
+  BaseRecalibrator \
+  --input ${bam} \
+  --output ${idSample}.recal.table \
+	--TMP_DIR /tmp \
   -R ${genomeFile} \
-  -I ${bam} \
   -L ${intervals} \
-  --disable_auto_index_creation_and_locking_when_reading_rods \
-  -knownSites ${dbsnp} \
+  --known-sites ${dbsnp} \
   ${known} \
-  -nct ${task.cpus} \
-  -l INFO \
-  -o ${idSample}.recal.table
+  --verbosity INFO
   """
 }
+
 // Create a TSV file to restart from this step
 recalibrationTableTSV.map { idPatient, status, idSample, bam, bai, recalTable ->
   gender = patientGenders[idPatient]
-  "${idPatient}\t${gender}\t${status}\t${idSample}\t${directoryMap.nonRecalibrated}/${bam}\t${directoryMap.nonRecalibrated}/${bai}\t${directoryMap.nonRecalibrated}/${recalTable}\n"
+  "${idPatient}\t${gender}\t${status}\t${idSample}\t${directoryMap.duplicateMarked}/${bam}\t${directoryMap.duplicateMarked}/${bai}\t${directoryMap.duplicateMarked}/${recalTable}\n"
 }.collectFile(
-  name: 'nonRecalibrated.tsv', sort: true, storeDir: directoryMap.nonRecalibrated
+  name: 'duplicateMarked.tsv', sort: true, storeDir: directoryMap.duplicateMarked
 )
 
-recalibrationTable = realignedBamToJoin.join(recalibrationTable, by:[0,1,2])
+recalibrationTable = mdBamToJoin.join(recalibrationTable, by:[0,1,2])
 
 if (step == 'recalibrate') recalibrationTable = bamFiles
 
@@ -508,20 +380,20 @@ process RecalibrateBam {
     set idPatient, status, idSample, file("${idSample}.recal.bam"), file("${idSample}.recal.bai") into recalibratedBam, recalibratedBamForStats
     set idPatient, status, idSample, val("${idSample}.recal.bam"), val("${idSample}.recal.bai") into recalibratedBamTSV
 
-  // HaplotypeCaller can do BQSR on the fly, so do not create a
+  // GATK4 HaplotypeCaller can not do BQSR on the fly, so we have to create a
   // recalibrated BAM explicitly.
-  when: params.explicitBqsrNeeded && !params.onlyQC
+  when: !params.onlyQC
 
   script:
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T PrintReads \
+  gatk --java-options -Xmx${task.memory.toGiga()}g \
+  ApplyBQSR \
   -R ${genomeFile} \
-  -I ${bam} \
+  --input ${bam} \
+  --output ${idSample}.recal.bam \
   -L ${intervals} \
-  --BQSR ${recalibrationReport} \
-  -o ${idSample}.recal.bam
+	--create-output-bam-index true \
+	--bqsr-recal-file ${recalibrationReport} 
   """
 }
 // Creating a TSV file to restart from this step
@@ -622,17 +494,6 @@ process GetVersionGATK {
   script: QC.getVersionGATK()
 }
 
-process GetVersionPicard {
-  publishDir directoryMap.version, mode: 'link'
-  output: file("v_*.txt")
-  when: step == 'mapping' && !params.onlyQC
-
-  script:
-  """
-  echo "Picard version:"\$(java -jar \$PICARD_HOME/picard.jar MarkDuplicates --version 2>&1) > v_picard.txt
-  """
-}
-
 /*
 ================================================================================
 =                               F U N C T I O N S                              =
@@ -679,7 +540,6 @@ def defineReferenceMap() {
 def defineStepList() {
   return [
     'mapping',
-    'realign',
     'recalibrate'
   ]
 }
@@ -812,7 +672,6 @@ def helpMessage() {
   log.info "       Option to start workflow"
   log.info "       Possible values are:"
   log.info "         mapping (default, will start workflow with FASTQ files)"
-  log.info "         realign (will start workflow with non-realigned BAM files)"
   log.info "         recalibrate (will start workflow with non-recalibrated BAM files)"
   log.info "    --noReports"
   log.info "       Disable QC tools and MultiQC to generate a HTML report"
diff --git a/nextflow.config b/nextflow.config
index 9fdfe3ea38..4f6196a9fe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,7 +14,7 @@ manifest {
 }
 
 env {
-  NXF_OPTS="-Xms1g -Xmx4g"
+  NXF_OPTS="-Xms1g"
 }
 
 profiles {
diff --git a/scripts/do_all.sh b/scripts/do_all.sh
index e4780958a1..d0e693ff57 100755
--- a/scripts/do_all.sh
+++ b/scripts/do_all.sh
@@ -57,8 +57,8 @@ function toLower() {
 
 if [[ $TOOL = docker ]] && [[ GRCh37,GRCh38 =~ $GENOME ]]
 then
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers freebayes,gatk,gatk4,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers r-base,runallelecount,sarek,snpeff
     nextflow run buildContainers.nf -profile ${PROFILE} --verbose --docker ${PUSH} --repository ${REPOSITORY} --tag ${TAG} --containers snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 else
-    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers freebayes,gatk,gatk4,igvtools,mutect1,picard,qctools,r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
+    nextflow run buildContainers.nf -profile ${PROFILE} --verbose --singularity --repository ${REPOSITORY} --tag ${TAG} --containerPath containers/ --containers r-base,runallelecount,sarek,snpeff$(toLower ${GENOME}),vep$(toLower ${GENOME})
 fi
diff --git a/scripts/test.sh b/scripts/test.sh
index ac45d10ba8..bcd017d1f1 100755
--- a/scripts/test.sh
+++ b/scripts/test.sh
@@ -9,6 +9,18 @@ SAMPLE=Sarek-data/testdata/tsv/tiny.tsv
 TEST=ALL
 TRAVIS=${TRAVIS:-false}
 
+TMPDIR=`pwd`/tmp
+mkdir -p $TMPDIR
+export NXF_SINGULARITY_CACHEDIR=$TMPDIR
+export NXF_TEMP=$TMPDIR
+
+export SINGULARITY_TMPDIR=$TMPDIR
+export SINGULARITY_CACHEDIR=$TMPDIR
+
+
+# remove Reference directory
+rm -rf References
+
 while [[ $# -gt 0 ]]
 do
   key=$1
@@ -91,7 +103,6 @@ fi
 if [[ ALL,STEP =~ $TEST ]]
 then
   run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal
-  run_wrapper --germline --step realign --noReports
   run_wrapper --germline --step recalibrate --noReports
   clean_repo
 fi
@@ -104,7 +115,7 @@ fi
 
 if [[ ALL,TOOLS =~ $TEST ]]
 then
-  run_wrapper --somatic --sample $SAMPLE --variantCalling  --tools FreeBayes,HaplotypeCaller,MuTect1,MuTect2
+  run_wrapper --somatic --sample $SAMPLE --variantCalling  --tools FreeBayes,HaplotypeCaller,Mutect2
 fi
 
 if [[ ALL,MANTA =~ $TEST ]]
diff --git a/somaticVC.nf b/somaticVC.nf
index c282b8467e..0e2347bb0e 100644
--- a/somaticVC.nf
+++ b/somaticVC.nf
@@ -29,10 +29,9 @@ kate: syntax groovy; space-indent on; indent-width 2;
  - RunSamtoolsStats - Run Samtools stats on recalibrated BAM files
  - RunBamQC - Run qualimap BamQC on recalibrated BAM files
  - CreateIntervalBeds - Create and sort intervals into bed files
- - RunMutect1 - Run MuTect1 for Variant Calling (Parallelized processes)
  - RunMutect2 - Run MuTect2 for Variant Calling (Parallelized processes)
  - RunFreeBayes - Run FreeBayes for Variant Calling (Parallelized processes)
- - ConcatVCF - Merge results from MuTect1 and MuTect2
+ - ConcatVCF - Merge results from paralellized variant callers
  - RunStrelka - Run Strelka for Variant Calling
  - RunManta - Run Manta for Structural Variant Calling
  - RunSingleManta - Run Manta for Single Structural Variant Calling
@@ -70,15 +69,12 @@ referenceMap = defineReferenceMap()
 toolList = defineToolList()
 
 if (!SarekUtils.checkReferenceMap(referenceMap)) exit 1, 'Missing Reference file(s), see --help for more information'
-if (!checkParameterList(tools,toolList)) exit 1, 'Unknown tool(s), see --help for more information'
+if (!SarekUtils.checkParameterList(tools,toolList)) exit 1, 'Unknown tool(s), see --help for more information'
 
 if (params.test && params.genome in ['GRCh37', 'GRCh38']) {
   referenceMap.intervals = file("$workflow.projectDir/repeats/tiny_${params.genome}.list")
 }
 
-// TODO
-// MuTect and Mutect2 could be run without a recalibrated BAM (they support
-// the --BQSR option), but this is not implemented, yet.
 // TODO
 // FreeBayes does not need recalibrated BAMs, but we need to test whether
 // the channels are set up correctly when we disable it
@@ -200,10 +196,9 @@ bamsTumor = bamsTumor.map { idPatient, status, idSample, bam, bai -> [idPatient,
 
 // We know that MuTect2 (and other somatic callers) are notoriously slow.
 // To speed them up we are chopping the reference into smaller pieces.
-// (see repeats/centromeres.list).
 // Do variant calling by this intervals, and re-merge the VCFs.
-// Since we are on a cluster, this can parallelize the variant call processes.
-// And push down the variant call wall clock time significanlty.
+// Since we are on a cluster or a multi-CPU machine, this can parallelize the 
+// variant call processes and push down the variant call wall clock time significanlty.
 
 process CreateIntervalBeds {
   tag {intervals.fileName}
@@ -285,48 +280,10 @@ bamsAll = bamsAll.map {
 
 bamsTumorNormalIntervals = bamsAll.spread(bedIntervals)
 
-// MuTect1, MuTect2, FreeBayes
-(bamsFMT1, bamsFMT2, bamsFFB) = bamsTumorNormalIntervals.into(3)
-
-process RunMutect1 {
-  tag {idSampleTumor + "_vs_" + idSampleNormal + "-" + intervalBed.baseName}
-
-  input:
-    set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor), file(intervalBed) from bamsFMT1
-    set file(genomeFile), file(genomeIndex), file(genomeDict), file(dbsnp), file(dbsnpIndex), file(cosmic), file(cosmicIndex) from Channel.value([
-      referenceMap.genomeFile,
-      referenceMap.genomeIndex,
-      referenceMap.genomeDict,
-      referenceMap.dbsnp,
-      referenceMap.dbsnpIndex,
-      referenceMap.cosmic,
-      referenceMap.cosmicIndex
-    ])
-
-  output:
-    set val("mutect1"), idPatient, idSampleNormal, idSampleTumor, file("${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf") into mutect1Output
-
-  when: 'mutect1' in tools && !params.onlyQC
-
-  script:
-  """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$MUTECT_HOME/muTect.jar \
-  -T MuTect \
-  -R ${genomeFile} \
-  --cosmic ${cosmic} \
-  --dbsnp ${dbsnp} \
-  -I:normal ${bamNormal} \
-  -I:tumor ${bamTumor} \
-  -L ${intervalBed} \
-  --disable_auto_index_creation_and_locking_when_reading_rods \
-  --out ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.call_stats.out \
-  --vcf ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
-  """
-}
-
-mutect1Output = mutect1Output.groupTuple(by:[0,1,2,3])
+// MuTect2, FreeBayes
+( bamsFMT2, bamsFFB) = bamsTumorNormalIntervals.into(3)
 
+// This will give as a list of unfiltered calls for MuTect2. 
 process RunMutect2 {
   tag {idSampleTumor + "_vs_" + idSampleNormal + "-" + intervalBed.baseName}
 
@@ -349,19 +306,18 @@ process RunMutect2 {
 
   script:
   """
-  java -Xmx${task.memory.toGiga()}g \
-  -jar \$GATK_HOME/GenomeAnalysisTK.jar \
-  -T MuTect2 \
-  -R ${genomeFile} \
-  --cosmic ${cosmic} \
-  --dbsnp ${dbsnp} \
-  -I:normal ${bamNormal} \
-  -I:tumor ${bamTumor} \
-  --disable_auto_index_creation_and_locking_when_reading_rods \
-  -L ${intervalBed} \
-  -o ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
+	gatk --java-options "-Xmx${task.memory.toGiga()}g" \
+		Mutect2 \
+		-R ${genomeFile}\
+		-I ${bamTumor}  -tumor ${idSampleTumor} \
+		-I ${bamNormal} -normal ${idSampleNormal} \
+		-L ${intervalBed} \
+		-O ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf
   """
 }
+//		--germline_resource af-only-gnomad.vcf.gz \
+//		--normal_panel pon.vcf.gz \
+//		--dbsnp ${dbsnp} \
 
 mutect2Output = mutect2Output.groupTuple(by:[0,1,2,3])
 
@@ -371,6 +327,7 @@ process RunFreeBayes {
   input:
     set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor), file(intervalBed) from bamsFFB
     file(genomeFile) from Channel.value(referenceMap.genomeFile)
+    file(genomeIndex) from Channel.value(referenceMap.genomeIndex)
 
   output:
     set val("freebayes"), idPatient, idSampleNormal, idSampleTumor, file("${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf") into freebayesOutput
@@ -400,7 +357,7 @@ freebayesOutput = freebayesOutput.groupTuple(by:[0,1,2,3])
 // we are merging the VCFs that are called separatelly for different intervals
 // so we can have a single sorted VCF containing all the calls for a given caller
 
-vcfsToMerge = mutect1Output.mix(mutect2Output, freebayesOutput)
+vcfsToMerge = mutect2Output.mix(freebayesOutput)
 if (params.verbose) vcfsToMerge = vcfsToMerge.view {
   "VCFs To be merged:\n\
   Tool  : ${it[0]}\tID    : ${it[1]}\tSample: [${it[3]}, ${it[2]}]\n\
@@ -419,12 +376,13 @@ process ConcatVCF {
   output:
     set variantCaller, idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into vcfConcatenated
 
-  when: ('mutect1' in tools || 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC
+  when: ( 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC
 
   script:
   outputFile = "${variantCaller}_${idSampleTumor}_vs_${idSampleNormal}.vcf"
 
   """
+	set -euo pipefail
   # first make a header from one of the VCF intervals
   # get rid of interval information only from the GATK command-line, but leave the rest
   FIRSTVCF=\$(ls *.vcf | head -n 1)
@@ -492,7 +450,7 @@ process RunStrelka {
 
   script:
   """
-  \$STRELKA_INSTALL_PATH/bin/configureStrelkaSomaticWorkflow.py \
+  configureStrelkaSomaticWorkflow.py \
   --tumor ${bamTumor} \
   --normal ${bamNormal} \
   --referenceFasta ${genomeFile} \
@@ -538,7 +496,7 @@ process RunManta {
 
   script:
   """
-  \$MANTA_INSTALL_PATH/bin/configManta.py \
+  configManta.py \
   --normalBam ${bamNormal} \
   --tumorBam ${bamTumor} \
   --reference ${genomeFile} \
@@ -591,7 +549,7 @@ process RunSingleManta {
 
   script:
   """
-  \$MANTA_INSTALL_PATH/bin/configManta.py \
+  configManta.py \
   --tumorBam ${bam} \
   --reference ${genomeFile} \
   --runDir Manta
@@ -620,6 +578,7 @@ if (params.verbose) singleMantaOutput = singleMantaOutput.view {
   Index : ${it[4].fileName}"
 }
 
+// Running Strelka Best Practice with Manta indel candidates
 // For easier joining, remaping channels to idPatient, idSampleNormal, idSampleTumor...
 
 bamsForStrelkaBP = bamsForStrelkaBP.map {
@@ -650,7 +609,7 @@ process RunStrelkaBP {
 
   script:
   """
-  \$STRELKA_INSTALL_PATH/bin/configureStrelkaSomaticWorkflow.py \
+  configureStrelkaSomaticWorkflow.py \
   --tumor ${bamTumor} \
   --normal ${bamNormal} \
   --referenceFasta ${genomeFile} \
@@ -932,36 +891,11 @@ def checkParameterExistence(it, list) {
   return true
 }
 
-def checkParameterList(list, realList) {
-  // Loop through all parameters to check their existence and spelling
-  return list.every{ checkParameterExistence(it, realList) }
-}
-
 def checkParamReturnFile(item) {
   params."${item}" = params.genomes[params.genome]."${item}"
   return file(params."${item}")
 }
 
-def checkReferenceMap(referenceMap) {
-  // Loop through all the references files to check their existence
-  referenceMap.every {
-    referenceFile, fileToCheck ->
-    checkRefExistence(referenceFile, fileToCheck)
-  }
-}
-
-def checkRefExistence(referenceFile, fileToCheck) {
-  if (fileToCheck instanceof List) return fileToCheck.every{ checkRefExistence(referenceFile, it) }
-  def f = file(fileToCheck)
-  // this is an expanded wildcard: we can assume all files exist
-  if (f instanceof List && f.size() > 0) return true
-  else if (!f.exists()) {
-    log.info  "Missing references: ${referenceFile} ${fileToCheck}"
-    return false
-  }
-  return true
-}
-
 def checkUppmaxProject() {
   // check if UPPMAX project number is specified
   return !(workflow.profile == 'slurm' && !params.project)
@@ -994,7 +928,6 @@ def defineToolList() {
     'freebayes',
     'haplotypecaller',
     'manta',
-    'mutect1',
     'mutect2',
     'strelka'
   ]
@@ -1027,7 +960,6 @@ def helpMessage() {
   log.info "       Option to configure which tools to use in the workflow."
   log.info "         Different tools to be separated by commas."
   log.info "       Possible values are:"
-  log.info "         mutect1 (use MuTect1 for VC)"
   log.info "         mutect2 (use MuTect2 for VC)"
   log.info "         freebayes (use FreeBayes for VC)"
   log.info "         strelka (use Strelka for VC)"