diff --git a/README.md b/README.md
index c421539..c8811e1 100644
--- a/README.md
+++ b/README.md
@@ -1 +1 @@
-# NGS_RNA
+# NGS_RNA 
diff --git a/generate_template.sh b/generate_template.sh
index 462666f..129df54 100755
--- a/generate_template.sh
+++ b/generate_template.sh
@@ -4,12 +4,11 @@ module load NGS_RNA/3.2.4-Molgenis-Compute-v16.05.1-Java-1.8.0_45
 module list
 
 HOST=$(hostname)
-##Running script for checking the environment variables
-sh ${EBROOTNGS_RNA}/checkEnvironment.sh ${HOST}
+thisDir=$(pwd)
 
-ENVIRONMENT=$(awk '{print $1}' ./environment_checks.txt)
-TMPDIR=$(awk '{print $2}' ./environment_checks.txt)
-GROUP=$(awk '{print $3}' ./environment_checks.txt)
+ENVIRONMENT="parameters.${HOST%%.*}.csv"
+TMPDIRECTORY=$(basename $(cd ../../ && pwd ))
+GROUP=$(basename $(cd ../../../ && pwd ))
 
 PROJECT="PROJECTNAME"
 RUNID="run01"
diff --git a/parameters.boxy.csv b/parameters.boxy.csv
new file mode 100755
index 0000000..5f5c5b1
--- /dev/null
+++ b/parameters.boxy.csv
@@ -0,0 +1,8 @@
+#### ENVIRONMENT VARIABLES ####
+queue,gaf
+workDir,/groups/umcg-gaf/
+dataDir,${root}/data/
+tmpName,tmp03
+root,/apps/
+tempDir,${workDir}/${tmpName}/tmp/
+permanentDir,${workDir}/prm03
diff --git a/parameters.csv b/parameters.csv
index 6f1da88..e4c5521 100755
--- a/parameters.csv
+++ b/parameters.csv
@@ -6,18 +6,18 @@ jobname,jobname
 ##### Tools and versions #####
 jdkVersion,Java/1.7.0_80
 NGSUtilsVersion,ngs-utils
-NGSRNAVersion,NGS_RNA/3.2.3-Molgenis-Compute-v16.05.1-Java-1.8.0_45
+NGSRNAVersion,NGS_RNA/3.2.4
 fastqcVersion,FastQC/0.11.3-Java-1.7.0_80
-samtoolsVersion,SAMtools/1.2-goolf-1.7.20
+samtoolsVersion,SAMtools/1.2-foss-2015b
 RVersion,R/3.2.1-goolf-1.7.20
 wkhtmltopdfVersion,wkhtmltopdf/0.11.0_rc1-static-amd64
 picardVersion,picard/1.130-Java-1.7.0_80
 anacondaVersion,Anaconda/1.8.0-Linux-x86_64
 htseqVersion,HTSeq/0.6.1p1
-hisatVersion,hisat/0.1.5-beta-goolf-1.7.20
+hisatVersion,hisat/0.1.5-beta-foss-2015b
 pythonVersion,Python/2.7.9-goolf-1.7.20
-gatkVersion,GATK/3.4-46-Java-1.7.0_80 
-ghostscriptVersion,Ghostscript/9.16-goolf-1.7.20
+gatkVersion,GATK/3.6-Java-1.8.0_74
+ghostscriptVersion,Ghostscript/9.16-foss-2015b
 kallistoVersion,Kallisto/0.43.0-goolf-1.7.20
 BBMapVersion,BBMap/35.69-Java-1.7.0_80
 picardJar,picard.jar
diff --git a/parameters.homo_sapiens.csv b/parameters.homo_sapiens.csv
index 55e7726..ae962ab 100755
--- a/parameters.homo_sapiens.csv
+++ b/parameters.homo_sapiens.csv
@@ -6,7 +6,7 @@ indexFolderName,human_g1k_v37
 dbSNPFileID,dbsnp_138.${genome}
 indicesDir,${dataDir}/ftp.broadinstitute.org/bundle/2.8/${genome}/
 dbSNPDir,${dataDir}/dbSNP/
-hisatIndex,${dataDir}/ftp.broadinstitute.org/bundle/2.8/${genome}/${hisatVersion}/${indexFolderName}
+hisatIndex,${dataDir}/ftp.broadinstitute.org/bundle/2.8/${genome}/hisat/0.1.5-beta-goolf-1.7.20/${indexFolderName}
 kallistoIndex,${dataDir}/ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/Homo_sapiens.GRCh37.75.cdna.all.fa.idx
 indexFileFastaIndex,${indexSpecies}.fai
 indexSpecies,${indicesDir}/${indexFileID}.fasta
diff --git a/protocols/CreateExternSamplesProjects.sh b/protocols/CreateExternSamplesProjects.sh
index e94c136..f6c59a8 100755
--- a/protocols/CreateExternSamplesProjects.sh
+++ b/protocols/CreateExternSamplesProjects.sh
@@ -11,6 +11,7 @@
 #string jdkVersion
 #string groupname
 #string NGSUtilsVersion
+#string NGSRNAVersion
 #list sequencingStartDate
 #list sequencer
 #list run
@@ -36,7 +37,7 @@
 
 umask 0007
 module load Molgenis-Compute/${computeVersion}
-module load ngs-utils/16.09.1
+module load ${NGSUtilsVersion}
 
 module list
 #
@@ -96,7 +97,7 @@ cd $ROCKETPOINT
 
 echo "before splitting"
 echo `pwd`
-module load ${ngsUtilsVersion}
+module load ${NGSRNAVersion}
 
 #
 # TODO: array for each sample:
diff --git a/protocols/HisatAlignment.sh b/protocols/HisatAlignment.sh
index 2243bd5..407ae00 100644
--- a/protocols/HisatAlignment.sh
+++ b/protocols/HisatAlignment.sh
@@ -54,9 +54,6 @@ tmpSortedBai=${MC_tmpFile}
 
 #Load modules
 ${stage} ${hisatVersion}
-${stage} ${samtoolsVersion}
-${stage} ${picardVersion}
-
 #check modules
 ${checkStage}
 
@@ -75,6 +72,11 @@ echo "## "$(date)" Start $0"
 	perl -nle 'print $2,"|\t",$1 while (m%^[ ]*([.0-9\%]+\s\(.+\)|[.0-9\%]+).(.+)%g);' ${intermediateDir}/${externalSampleID}_L${lane}.hisat.log > ${intermediateDir}/${externalSampleID}_L${lane}.hisat.final.log
 
 
+${stage} ${picardVersion}
+
+#check modules
+${checkStage}
+
 java -XX:ParallelGCThreads=4 -jar -Xmx6g ${EBROOTPICARD}/${picardJar} SortSam \
 	INPUT=${tmpAlignedSam} \
 	OUTPUT=${tmpSortedBam} \
diff --git a/test/autotest_generate_template.sh b/test/autotest_generate_template.sh
index 3c391a4..f02dbd8 100755
--- a/test/autotest_generate_template.sh
+++ b/test/autotest_generate_template.sh
@@ -60,7 +60,7 @@ sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh \
 -o "workflowpath=${WORKFLOW};outputdir=scripts/jobs;\
 groupname=${GROUP};\
 mainParameters=${WORKDIR}/generatedscripts/${PROJECT}/parameters.csv;\
-ngsversion='NGS_RNA/3.2.4-Molgenis-Compute-v16.05.1-Java-1.8.0_45';\
+ngsversion='NGS_RNA/3.2.4';\
 worksheet=${WORKDIR}/generatedscripts/${PROJECT}/${PROJECT}.csv;\
 parameters_build=${WORKDIR}/generatedscripts/${PROJECT}/parameters.${BUILD}.csv;\
 parameters_species=${WORKDIR}/generatedscripts/${PROJECT}/parameters.${SPECIES}.csv;\
diff --git a/test/results/PlatinumSubset_NGS_RNA.variant.calls.genotyped.chr1.true.vcf b/test/results/PlatinumSubset_NGS_RNA.variant.calls.genotyped.chr1.true.vcf
index e9f0536..e7e488d 100644
--- a/test/results/PlatinumSubset_NGS_RNA.variant.calls.genotyped.chr1.true.vcf
+++ b/test/results/PlatinumSubset_NGS_RNA.variant.calls.genotyped.chr1.true.vcf
@@ -1,7 +1,7 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
 ##FILTER=<ID=LowQual,Description="Low quality">
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
@@ -11,9 +11,9 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##GATKCommandLine.CombineGVCFs=<ID=CombineGVCFs,Version=3.4-46-gbc02625,Date="Tue Oct 11 16:03:24 CEST 2016",Epoch=1476194604604,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[/apps//data//ftp.broadinstitute.org/bundle/2.8/b37//human_g1k_v37.chr1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/groups/umcg-gaf//tmp04/tmp//PlatinumSubset_NGS_RNA/run01//PlatinumSample.GatkHaplotypeCallerGvcf.g.vcf)])] out=/groups/umcg-gaf/tmp04/tmp/PlatinumSubset_NGS_RNA/run01/tmp_s08b_GatkMergeGvcf_0.sh_0d56712abb112e6994824b55163fd392/PlatinumSubset_NGS_RNA.variant.calls.combined.chr1.g.vcf.0 convertToBasePairResolution=false breakBandsAtMultiplesOf=0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.4-46-gbc02625,Date="Tue Oct 11 16:04:15 CEST 2016",Epoch=1476194655208,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[1:1-1200000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/groups/umcg-gaf//tmp04/tmp//PlatinumSubset_NGS_RNA/run01//PlatinumSubset_NGS_RNA.variant.calls.combined.chr1.g.vcf.0)])] out=/groups/umcg-gaf/tmp04/tmp/PlatinumSubset_NGS_RNA/run01/tmp_s08c_GatkGenotypeGvcf_0.sh_35b8e882b9bae697c32b3be41d11f71c/PlatinumSubset_NGS_RNA.variant.calls.genotyped.chr1.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=20.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, StrandOddsRatio] dbsnp=(RodBinding name=dbsnp source=/apps//data//dbSNP/dbsnp_138.b37.vcf) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-46-gbc02625,Date="Tue Oct 11 16:01:27 CEST 2016",Epoch=1476194487060,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/groups/umcg-gaf//tmp04/tmp//PlatinumSubset_NGS_RNA/run01/PlatinumSample.sorted.merged.dedup.splitAndTrim.realigned.bqsr.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[1:1-1200000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/apps//data//dbSNP/dbsnp_138.b37.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=true captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.CombineGVCFs=<ID=CombineGVCFs,Version=3.6-0-g89b7209,Date="Wed Jan 11 14:49:03 CET 2017",Epoch=1484142543879,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/apps//data//ftp.broadinstitute.org/bundle/2.8/b37//human_g1k_v37.chr1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false annotation=[AS_RMSMappingQuality] dbsnp=(RodBinding name= source=UNBOUND) variant=[(RodBindingCollection [(RodBinding name=variant source=/groups/umcg-gaf//tmp04/tmp//PlatinumSubset_NGS_RNA/run01//PlatinumSample.GatkHaplotypeCallerGvcf.g.vcf)])] out=/groups/umcg-gaf/tmp04/tmp/PlatinumSubset_NGS_RNA/run01/tmp_s08b_GatkMergeGvcf_0.sh_6775bbbc552deeaf0914ccb73041caba/PlatinumSubset_NGS_RNA.variant.calls.combined.chr1.g.vcf.0 convertToBasePairResolution=false breakBandsAtMultiplesOf=0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.6-0-g89b7209,Date="Wed Jan 11 14:49:29 CET 2017",Epoch=1484142569400,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1:1-1200000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/groups/umcg-gaf//tmp04/tmp//PlatinumSubset_NGS_RNA/run01//PlatinumSubset_NGS_RNA.variant.calls.combined.chr1.g.vcf.0)])] out=/groups/umcg-gaf/tmp04/tmp/PlatinumSubset_NGS_RNA/run01/tmp_s08c_GatkGenotypeGvcf_0.sh_808556667e9a5fa0b48e2fb257a9cddd/PlatinumSubset_NGS_RNA.variant.calls.genotyped.chr1.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=20.0 max_alternate_alleles=6 max_num_PL_values=100 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name=dbsnp source=/apps//data//dbSNP/dbsnp_138.b37.vcf) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.6-0-g89b7209,Date="Wed Jan 11 14:47:07 CET 2017",Epoch=1484142427226,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/groups/umcg-gaf//tmp04/tmp//PlatinumSubset_NGS_RNA/run01/PlatinumSample.sorted.merged.dedup.splitAndTrim.realigned.bqsr.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[1:1-1200000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/apps//data//dbSNP/dbsnp_138.b37.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=true captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
 ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
 ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
 ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
@@ -88,6 +88,7 @@
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
 ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
 ##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
@@ -96,6 +97,7 @@
 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
 ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
 ##contig=<ID=1,length=249250621,assembly=b37>
@@ -184,205 +186,203 @@
 ##contig=<ID=GL000192.1,length=547496,assembly=b37>
 ##reference=file:///apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PlatinumSample
-1	14653	rs375086259	C	T	1895.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.808e+00;ClippingRankSum=-5.500e-02;DB;DP=112;FS=41.098;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-2.221e+00;QD=16.93;ReadPosRankSum=0.935;SOR=5.766	GT:AD:DP:GQ:PL	0/1:54,58:112:99:1924,0,1621
-1	14677	rs201327123	G	A	2477.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;ClippingRankSum=1.39;DB;DP=151;FS=43.630;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-2.000e-03;QD=16.63;ReadPosRankSum=3.50;SOR=3.320	GT:AD:DP:GQ:PL	0/1:68,81:149:99:2506,0,1756
-1	14907	rs79585140	A	G	255.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-8.250e-01;ClippingRankSum=-1.768e+00;DB;DP=11;FS=7.404;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.296e+00;QD=23.25;ReadPosRankSum=-3.540e-01;SOR=1.155	GT:AD:DP:GQ:PL	0/1:2,9:11:44:284,0,44
-1	14930	rs75454623	A	G	365.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.76;ClippingRankSum=-1.768e+00;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.06;QD=26.13;ReadPosRankSum=2.19;SOR=1.085	GT:AD:DP:GQ:PL	0/1:4,10:14:57:394,0,57
-1	14933	rs199856693	G	A	242.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.965;ClippingRankSum=-3.860e-01;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.471;QD=17.34;ReadPosRankSum=1.47;SOR=1.179	GT:AD:DP:GQ:PL	0/1:6,8:14:99:271,0,219
-1	14976	rs71252251	G	A	142.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-6.840e-01;ClippingRankSum=-6.840e-01;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-6.840e-01;QD=17.85;ReadPosRankSum=0.322;SOR=0.799	GT:AD:DP:GQ:PL	0/1:3,5:8:97:171,0,97
-1	15118	rs71252250	A	G	173.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.708e+00;ClippingRankSum=-5.660e-01;DB;DP=11;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-3.820e-01;QD=15.80;ReadPosRankSum=-5.660e-01;SOR=0.132	GT:AD:DP:GQ:PL	0/1:3,8:11:87:202,0,87
-1	15211	rs78601809	T	G	404.77	.	AC=2;AF=1.00;AN=2;DB;DP=13;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.14;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,13:13:39:433,39,0
-1	15274	rs201931625	A	T	203.84	.	AC=2;AF=1.00;AN=2;DB;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.97;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,6:6:18:232,18,0
-1	15447	rs201635489	A	G	192.80	.	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.54;SOR=4.174	GT:AD:DP:GQ:PL	1/1:0,7:7:21:221,21,0
-1	16257	rs78588380	G	C	29.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026e+00;ClippingRankSum=-1.026e+00;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.026e+00;QD=7.44;ReadPosRankSum=1.03;SOR=0.693	GT:AD:DP:GQ:PL	0/1:2,2:4:58:58,0,65
-1	16378	rs148220436	T	C	78.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.23;ClippingRankSum=1.23;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.358;QD=15.75;ReadPosRankSum=0.358;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,3:5:64:107,0,64
-1	16495	rs141130360	G	C	329.56	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.19;ClippingRankSum=0.091;DB;DP=14;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.100e-02;QD=23.54;ReadPosRankSum=1.55;SOR=1.022	GT:AD:DP:GQ:PL	0/1:2,12:14:7:357,0,7
-1	16571	rs199676946	G	A	21.80	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.720e-01;ClippingRankSum=1.07;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.59;QD=2.72;ReadPosRankSum=1.07;SOR=0.693	GT:AD:DP:GQ:PL	0/1:6,2:8:50:50,0,205
-1	20037	.	A	C	34.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;ClippingRankSum=-1.231e+00;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.358;QD=6.95;ReadPosRankSum=1.23;SOR=1.609	GT:AD:DP:GQ:PL	0/1:3,2:5:63:63,0,69
-1	20129	rs202081272	C	T	33.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=0.720;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.720;QD=5.63;ReadPosRankSum=0.00;SOR=1.179	GT:AD:DP:GQ:PL	0/1:4,2:6:62:62,0,93
-1	127573	rs199894737	G	A	128.03	.	AC=2;AF=1.00;AN=2;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.01;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,4:4:12:156,12,0
-1	136052	.	T	C	163.03	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;ClippingRankSum=0.747;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.747;QD=20.38;ReadPosRankSum=0.747;SOR=0.693	GT:AD:DP:GQ:PL	0/1:1,7:8:12:191,0,12
-1	136145	.	T	C	190.84	.	AC=2;AF=1.00;AN=2;DP=6;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.81;SOR=1.329	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,6:6:18:1|1:136145_T_C:219,18,0
-1	136176	.	T	C	107.28	.	AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.24;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:136145_T_C:135,9,0
-1	136178	.	T	C	107.28	.	AC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.63;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:136145_T_C:135,9,0
-1	136768	.	T	C	57.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.580e-01;ClippingRankSum=0.358;DP=5;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.358;QD=11.55;ReadPosRankSum=-3.580e-01;SOR=2.833	GT:AD:DP:GQ:PL	0/1:2,3:5:57:86,0,57
-1	137635	.	T	C	21.80	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.580e-01;ClippingRankSum=0.358;DP=5;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.231e+00;QD=4.36;ReadPosRankSum=-3.580e-01;SOR=2.245	GT:AD:DP:GQ:PGT:PID:PL	0/1:3,2:5:50:0|1:137635_T_C:50,0,110
-1	139213	rs370723703	A	G	85.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.736;QD=28.59;ReadPosRankSum=-7.360e-01;SOR=1.179	GT:AD:DP:GQ:PGT:PID:PL	0/1:1,2:3:67:0|1:139213_A_G:114,0,67
-1	139233	rs373847457	C	A	82.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-3.580e-01;ClippingRankSum=-1.231e+00;DB;DP=5;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-3.580e-01;QD=16.55;ReadPosRankSum=1.23;SOR=1.179	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,3:5:99:0|1:139213_A_G:111,0,104
-1	228534	.	T	C	95.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.70;ClippingRankSum=0.077;DP=13;FS=2.522;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-2.310e-01;QD=7.37;ReadPosRankSum=2.08;SOR=1.546	GT:AD:DP:GQ:PL	0/1:9,4:13:99:124,0,225
-1	521603	rs199602814	G	A	21.77	.	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
-1	564598	rs6594028	A	G	344.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.72;ClippingRankSum=-1.975e+00;DB;DP=22;FS=1.740;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.228;QD=17.24;ReadPosRankSum=0.304;SOR=0.368	GT:AD:DP:GQ:PL	0/1:9,11:20:99:373,0,107
-1	564654	rs147404388	G	A	29.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.387;DB;DP=59;FS=13.201;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-9.490e-01;QD=0.50;ReadPosRankSum=0.310;SOR=0.487	GT:AD:DP:GQ:PL	0/1:52,7:59:58:58,0,1089
-1	565286	rs1578391	C	T	69880.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=5.53;ClippingRankSum=-4.350e-01;DB;DP=2108;FS=3.011;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.166;QD=33.78;ReadPosRankSum=6.24;SOR=0.007	GT:AD:DP:GQ:PL	1/1:27,2042:2071:99:69909,5615,0
-1	565406	rs6594029	C	T	4626.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=5.57;ClippingRankSum=0.637;DB;DP=217;FS=9.181;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.210;QD=26.44;ReadPosRankSum=-6.494e+00;SOR=3.409	GT:AD:DP:GQ:PL	1/1:28,147:175:30:4655,30,0
-1	565433	rs9701055	C	T	1102.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.63;ClippingRankSum=-8.420e-01;DB;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.446;QD=31.51;ReadPosRankSum=0.941;SOR=2.833	GT:AD:DP:GQ:PL	1/1:1,34:35:94:1131,94,0
-1	565508	rs9283150	G	A	40.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=20.37;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:68,6,0
-1	565541	rs6594031	A	G	239.80	.	AC=2;AF=1.00;AN=2;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.26;SOR=4.174	GT:AD:DP:GQ:PL	1/1:0,7:7:21:268,21,0
-1	565697	rs3021087	A	G	91.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.93;ClippingRankSum=1.47;DB;DP=70;FS=5.775;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.298;QD=1.31;ReadPosRankSum=-1.316e+00;SOR=0.180	GT:AD:DP:GQ:PL	0/1:61,9:70:99:120,0,1346
-1	565728	rs199661867	C	A	2963.77	.	AC=2;AF=1.00;AN=2;DB;DP=85;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.87;SOR=1.233	GT:AD:DP:GQ:PL	1/1:0,85:85:99:2992,255,0
-1	565870	rs9326619	T	C	750.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.08;ClippingRankSum=0.433;DB;DP=30;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.605e+00;QD=25.89;ReadPosRankSum=0.433;SOR=2.226	GT:AD:DP:GQ:PL	0/1:7,22:29:99:779,0,113
-1	565901	rs7411575	G	A	470.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.37;ClippingRankSum=0.024;DB;DP=27;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.268;QD=17.44;ReadPosRankSum=2.95;SOR=0.287	GT:AD:DP:GQ:PL	0/1:12,15:27:99:499,0,108
-1	565937	rs7417504	T	C	361.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.65;ClippingRankSum=0.406;DB;DP=24;FS=10.073;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.04;QD=15.07;ReadPosRankSum=2.03;SOR=0.027	GT:AD:DP:GQ:PL	0/1:11,13:24:83:390,0,83
-1	565976	rs9283151	C	T	388.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.56;ClippingRankSum=-2.960e-01;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.197;QD=21.60;ReadPosRankSum=2.66;SOR=0.495	GT:AD:DP:GQ:PL	0/1:5,13:18:49:417,0,49
-1	566024	rs6421779	G	A	63.80	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.727;QD=15.95;ReadPosRankSum=0.727;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/1:1,3:4:21:0|1:566024_G_A:92,0,21
-1	566037	.	T	C	63.80	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.270e-01;ClippingRankSum=-7.270e-01;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.270e-01;QD=15.95;ReadPosRankSum=0.727;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/1:1,3:4:21:0|1:566024_G_A:92,0,21
-1	566296	.	G	A	365.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=4.79;ClippingRankSum=2.07;DP=480;FS=1.554;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.290e+00;QD=0.84;ReadPosRankSum=3.82;SOR=0.961	GT:AD:DP:GQ:PL	0/1:387,49:466:99:394,0,11913
-1	566573	rs1856866	A	G	112.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.33;ClippingRankSum=0.799;DB;DP=95;FS=4.303;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.475;QD=1.25;ReadPosRankSum=-1.060e+00;SOR=0.287	GT:AD:DP:GQ:PL	0/1:78,12:93:99:141,0,1454
-1	566771	rs2185536	C	T	270.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=6.17;ClippingRankSum=0.370;DB;DP=137;FS=8.484;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.300e-02;QD=2.02;ReadPosRankSum=6.67;SOR=0.007	GT:AD:DP:GQ:PL	0/1:115,19:134:99:299,0,1772
-1	566792	rs9283152	T	C	641.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070e-01;ClippingRankSum=0.249;DB;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.070e-01;QD=24.68;ReadPosRankSum=2.88;SOR=1.765	GT:AD:DP:GQ:PL	0/1:4,22:26:35:670,0,35
-1	566816	rs2185537	C	A	41.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.58;ClippingRankSum=0.315;DB;DP=18;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.063;QD=2.46;ReadPosRankSum=-1.890e-01;SOR=0.283	GT:AD:DP:GQ:PL	0/1:14,3:17:70:70,0,133
-1	566916	rs3949348	A	G	39.85	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DB;DP=3;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.736;QD=13.28;ReadPosRankSum=0.736;SOR=1.179	GT:AD:DP:GQ:PL	0/1:1,2:3:17:68,0,17
-1	566960	rs2185540	T	C	41.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=20.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:69,6,0
-1	567002	rs9285834	T	C	72.89	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.727;QD=18.22;ReadPosRankSum=0.727;SOR=0.916	GT:AD:DP:GQ:PL	1/1:1,3:4:2:99,2,0
-1	567033	rs9326620	T	C	147.41	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;ClippingRankSum=0.736;DB;DP=6;FS=7.782;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.736;QD=24.57;ReadPosRankSum=0.736;SOR=3.590	GT:AD:DP:GQ:PL	1/1:1,5:6:8:175,8,0
-1	567062	rs9326621	C	T	151.79	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DB;DP=6;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.360e-01;QD=25.30;ReadPosRankSum=0.736;SOR=0.941	GT:AD:DP:GQ:PL	0/1:1,5:6:23:180,0,23
-1	567092	rs9326622	T	C	44.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.290e-01;ClippingRankSum=1.31;DB;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.88;QD=4.97;ReadPosRankSum=1.16;SOR=0.446	GT:AD:DP:GQ:PL	0/1:5,4:9:73:73,0,107
-1	567119	rs9283153	A	C	134.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.92;ClippingRankSum=-1.517e+00;DB;DP=8;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.322;QD=16.85;ReadPosRankSum=1.52;SOR=0.582	GT:AD:DP:GQ:PL	0/1:3,5:8:35:163,0,35
-1	567191	rs2185541	C	T	1799.88	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.57;ClippingRankSum=-1.155e+00;DB;DP=72;FS=10.262;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-2.820e-01;QD=26.47;ReadPosRankSum=-5.730e-01;SOR=3.778	GT:AD:DP:GQ:PL	0/1:8,60:71:16:1828,0,16
-1	567242	rs7518996	G	A	45667.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=3.20;ClippingRankSum=-9.230e-01;DB;DP=1662;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=-4.800e-02;QD=27.59;ReadPosRankSum=4.58;SOR=3.730	GT:AD:DP:GQ:PL	1/1:21,1634:1655:99:45696,4448,0
-1	567486	rs1972377	T	C	304.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.66;ClippingRankSum=-7.920e-01;DB;DP=23;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.550e-01;QD=15.24;ReadPosRankSum=1.35;SOR=0.693	GT:AD:DP:GQ:PL	0/1:7,13:20:99:333,0,191
-1	567579	rs112232512	C	T	3542.77	.	AC=2;AF=1.00;AN=2;DB;DP=99;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.09;SOR=3.500	GT:AD:DP:GQ:PL	1/1:0,98:98:99:3571,295,0
-1	567783	.	T	C	302.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.269;ClippingRankSum=0.00;DP=17;FS=6.990;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-6.730e-01;QD=18.92;ReadPosRankSum=0.538;SOR=0.838	GT:AD:DP:GQ:PL	0/1:3,13:16:28:331,0,28
-1	567807	rs2853819	T	C	329.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.02;ClippingRankSum=0.326;DB;DP=17;FS=3.222;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=1.37;QD=21.98;ReadPosRankSum=0.979;SOR=2.147	GT:AD:DP:GQ:PL	0/1:4,11:15:68:358,0,68
-1	567867	rs2000096	A	G	156.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=3.57;ClippingRankSum=-3.000e-02;DB;DP=79;FS=6.658;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.670e-01;QD=2.12;ReadPosRankSum=1.82;SOR=0.074	GT:AD:DP:GQ:PL	0/1:63,11:74:99:185,0,1161
-1	567997	.	C	CA	590.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.38;ClippingRankSum=-2.200e-02;DP=302;FS=4.220;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.434;QD=2.19;ReadPosRankSum=4.78;SOR=0.158	GT:AD:DP:GQ:PL	0/1:218,52:279:99:619,0,5984
-1	568201	rs4098611	T	C	370.77	.	AC=2;AF=1.00;AN=2;DB;DP=10;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.93;SOR=3.258	GT:AD:DP:GQ:PL	1/1:0,10:10:30:399,30,0
-1	568361	rs4098613	T	C	56.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;ClippingRankSum=-5.500e-01;DB;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.11;ReadPosRankSum=-5.500e-01;SOR=1.179	GT:AD:DP:GQ:PL	0/1:4,3:7:85:85,0,93
-1	568419	rs3905037	T	C	74.94	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;ClippingRankSum=0.727;DB;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.270e-01;QD=18.73;ReadPosRankSum=0.727;SOR=0.916	GT:AD:DP:GQ:PL	0/1:1,3:4:14:103,0,14
-1	568572	rs7413388	G	A	176.80	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.05;ClippingRankSum=-5.730e-01;DB;DP=9;FS=13.222;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.573;QD=19.64;ReadPosRankSum=2.05;SOR=2.204	GT:AD:DP:GQ:PL	0/1:3,6:9:21:205,0,21
-1	569004	rs9285835	T	C	85.28	.	AC=2;AF=1.00;AN=2;DB;DP=1;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.83;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,1:1:9:1|1:569004_T_C:113,9,0
-1	569010	rs9285836	T	C	124.90	.	AC=2;AF=1.00;AN=2;DB;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.98;SOR=3.611	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,5:5:15:1|1:569004_T_C:153,15,0
-1	569052	rs2153588	C	T	245.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;ClippingRankSum=0.929;DB;DP=12;FS=17.404;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.599e+00;QD=20.48;ReadPosRankSum=1.93;SOR=4.398	GT:AD:DP:GQ:PL	0/1:4,8:12:94:274,0,94
-1	569204	rs112660509	T	C	990.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.73;ClippingRankSum=0.322;DB;DP=48;FS=4.498;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.854;QD=22.52;ReadPosRankSum=-1.386e+00;SOR=1.981	GT:AD:DP:GQ:PL	0/1:10,34:44:99:1019,0,147
-1	569226	rs6594032	C	A	3215.74	.	AC=2;AF=1.00;AN=2;BaseQRankSum=6.60;ClippingRankSum=-7.400e-02;DB;DP=119;FS=2.211;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=-4.190e-01;QD=28.97;ReadPosRankSum=5.12;SOR=0.254	GT:AD:DP:GQ:PL	1/1:19,92:111:37:3244,37,0
-1	569267	rs6650105	G	A	20741.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=10.19;ClippingRankSum=0.091;DB;DP=756;FS=9.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.320;QD=30.28;ReadPosRankSum=9.63;SOR=3.405	GT:AD:DP:GQ:PL	1/1:69,616:706:99:20770,529,0
-1	569492	rs6594033	T	C	15176.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=6.44;ClippingRankSum=-7.710e-01;DB;DP=720;FS=16.526;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=-8.090e-01;QD=24.40;ReadPosRankSum=-1.064e+01;SOR=5.680	GT:AD:DP:GQ:PL	1/1:64,558:667:99:15205,307,0
-1	569624	rs6594035	T	C	145.56	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DB;DP=7;FS=7.782;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.360e-01;QD=24.26;ReadPosRankSum=-7.360e-01;SOR=3.590	GT:AD:DP:GQ:PL	0/1:1,5:6:7:173,0,7
-1	569803	rs2096045	G	A	183.10	.	AC=2;AF=1.00;AN=2;BaseQRankSum=0.742;ClippingRankSum=-7.420e-01;DB;DP=7;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=-7.420e-01;QD=26.16;ReadPosRankSum=-7.420e-01;SOR=1.179	GT:AD:DP:GQ:PL	1/1:1,6:7:11:211,11,0
-1	569873	.	A	T	49.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.500e-01;ClippingRankSum=0.00;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-5.500e-01;QD=7.11;ReadPosRankSum=0.550;SOR=1.179	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,3:7:78:0|1:569873_A_T:78,0,159
-1	569874	.	CAA	C	49.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;ClippingRankSum=0.550;DP=7;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=7.11;ReadPosRankSum=0.550;SOR=1.179	GT:AD:DP:GQ:PGT:PID:PL	0/1:4,3:7:78:0|1:569873_A_T:78,0,159
-1	569878	rs9283155	C	G	34.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;ClippingRankSum=1.38;DB;DP=6;FS=3.979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.720;QD=5.79;ReadPosRankSum=0.720;SOR=2.225	GT:AD:DP:GQ:PL	0/1:4,2:6:63:63,0,106
-1	662037	.	T	C	12.99	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.179e+00;ClippingRankSum=-7.620e-01;DP=9;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-1.179e+00;QD=1.44;ReadPosRankSum=1.18;SOR=0.132	GT:AD:DP:GQ:PL	0/1:7,2:9:41:41,0,241
-1	662837	.	T	C	31.78	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-7.270e-01;ClippingRankSum=0.727;DP=4;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=-7.270e-01;QD=7.94;ReadPosRankSum=-7.270e-01;SOR=1.609	GT:AD:DP:GQ:PL	0/1:1,3:4:29:60,0,29
-1	662874	.	T	C	152.03	.	AC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.67;SOR=3.258	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,4:4:12:1|1:662874_T_C:180,12,0
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+1	982573	rs3813192	C	T	33.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;ClippingRankSum=0.00;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=5.63;ReadPosRankSum=1.28;SOR=0.223	GT:AD:DP:GQ:PL	0/1:4,2:6:62:62,0,112
+1	982994	rs10267	T	C	388.77	.	AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.45;SOR=1.270	GT:AD:DP:GQ:PL	1/1:0,11:11:33:417,33,0
+1	984302	rs9442391	T	C	923.77	.	AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.04;SOR=0.770	GT:AD:DP:GQ:PL	1/1:0,25:25:75:952,75,0
+1	988503	rs2799071	A	T	21.77	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
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+1	990517	rs2710872	C	T	15106.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.76;ClippingRankSum=0.00;DB;DP=426;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=29.82;ReadPosRankSum=1.78;SOR=0.503	GT:AD:DP:GQ:PL	1/1:1,424:425:99:15135,1254,0
+1	990773	rs2799072	C	T	12785.77	.	AC=2;AF=1.00;AN=2;BaseQRankSum=1.78;ClippingRankSum=0.00;DB;DP=355;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=33.74;ReadPosRankSum=1.93;SOR=0.379	GT:AD:DP:GQ:PL	1/1:1,354:355:99:12814,1058,0
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+1	990839	rs13129	C	T	6052.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-5.317e+00;ClippingRankSum=0.00;DB;DP=357;ExcessHet=3.0103;FS=0.802;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.95;ReadPosRankSum=1.39;SOR=0.756	GT:AD:DP:GQ:PL	0/1:160,197:357:99:6081,0,4660
+1	990984	rs8014	G	A	14078.77	.	AC=2;AF=1.00;AN=2;DB;DP=393;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.93;SOR=0.887	GT:AD:DP:GQ:PL	1/1:0,393:393:99:14107,1181,0
+1	994391	rs2488991	G	T	124.03	.	AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.01;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,4:4:12:152,12,0
+1	995271	rs149372249	C	G	54.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.37;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:82,6,0
+1	999233	.	C	A	12.05	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=4.02;ReadPosRankSum=-4.310e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:32:40,0,32
+1	1000156	rs11584349	C	T	89.28	.	AC=2;AF=1.00;AN=2;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.76;SOR=1.179	GT:AD:DP:GQ:PL	1/1:0,3:3:9:117,9,0
+1	1001177	rs4970401	G	C	220.80	.	AC=2;AF=1.00;AN=2;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.54;SOR=0.941	GT:AD:DP:GQ:PL	1/1:0,7:7:21:249,21,0
+1	1001290	rs6665667	C	T	329.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190e+00;ClippingRankSum=0.00;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=25.37;ReadPosRankSum=-1.013e+00;SOR=0.859	GT:AD:DP:GQ:PL	0/1:2,11:13:42:358,0,42
+1	1002434	rs11260596	C	T	12.05	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=4.02;ReadPosRankSum=-9.670e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:29:40,0,29
+1	1017341	rs1133647	G	T	2335.77	.	AC=2;AF=1.00;AN=2;DB;DP=71;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.90;SOR=1.451	GT:AD:DP:GQ:PL	1/1:0,71:71:99:2364,213,0
+1	1017587	rs3766191	C	T	1160.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;ClippingRankSum=0.00;DB;DP=52;ExcessHet=3.0103;FS=4.983;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=22.32;ReadPosRankSum=0.237;SOR=1.609	GT:AD:DP:GQ:PL	0/1:12,40:52:99:1189,0,264
+1	1018144	rs9442395	T	C	381.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;ClippingRankSum=0.00;DB;DP=40;ExcessHet=3.0103;FS=4.743;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=9.54;ReadPosRankSum=-1.530e+00;SOR=0.477	GT:AD:DP:GQ:PL	0/1:25,15:40:99:410,0,807
+1	1018704	rs9442372	A	G	12.05	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=4.02;ReadPosRankSum=-9.670e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:31:40,0,31
+1	1026707	rs4074137	C	A	165.90	.	AC=2;AF=1.00;AN=2;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=33.18;SOR=1.022	GT:AD:DP:GQ:PL	1/1:0,5:5:15:194,15,0
+1	1026801	rs4562563	T	A	51.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
+1	1030633	rs6678318	G	A	21.77	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:49,6,0
+1	1060355	rs12567855	G	C	116.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;ClippingRankSum=0.00;DB;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=16.68;ReadPosRankSum=0.967;SOR=1.981	GT:AD:DP:GQ:PL	0/1:2,5:7:28:145,0,28
+1	1061508	rs12736814	G	A	39.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DB;DP=3;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=13.26;ReadPosRankSum=0.00;SOR=2.225	GT:AD:DP:GQ:PL	0/1:1,2:3:33:68,0,33
+1	1061602	rs34381538	G	A	43.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:71,6,0
+1	1096854	rs141182339	C	T	12.05	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DB;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=4.02;ReadPosRankSum=-9.670e-01;SOR=0.223	GT:AD:DP:GQ:PL	0/1:1,2:3:30:40,0,30
+1	1133077	rs2274789	A	G	43.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=0.524;ClippingRankSum=0.00;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.75;ReadPosRankSum=1.04;SOR=1.179	GT:AD:DP:GQ:PL	0/1:2,3:5:34:72,0,34
+1	1133254	rs12026794	G	A	71.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645e+00;ClippingRankSum=0.00;DB;DP=5;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.35;ReadPosRankSum=-5.240e-01;SOR=0.223	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,3:5:99:0|1:1133254_G_A:100,0,138
+1	1133273	rs12031928	T	C	49.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=12.44;ReadPosRankSum=0.00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	0/1:2,2:4:78:0|1:1133254_G_A:78,0,141
+1	1147007	.	T	A	42.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645e+00;ClippingRankSum=0.00;DP=5;ExcessHet=3.0103;FS=10.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=8.55;ReadPosRankSum=-1.645e+00;SOR=2.780	GT:AD:DP:GQ:PL	0/1:2,3:5:62:71,0,62
+1	1147422	rs17568	C	T	162.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=2.00;ClippingRankSum=0.00;DB;DP=16;ExcessHet=3.0103;FS=4.467;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.17;ReadPosRankSum=-5.800e-02;SOR=1.546	GT:AD:DP:GQ:PL	0/1:9,7:16:99:191,0,190
+1	1152408	rs74749446	C	T	16015.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=7.95;ClippingRankSum=0.00;DB;DP=770;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=20.88;ReadPosRankSum=1.65;SOR=0.724	GT:AD:DP:GQ:PL	0/1:266,501:767:99:16044,0,7018
+1	1155617	rs79598135	T	C	131.77	.	AC=1;AF=0.500;AN=2;BaseQRankSum=-1.856e+00;ClippingRankSum=0.00;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.64;ReadPosRankSum=0.508;SOR=0.368	GT:AD:DP:GQ:PL	0/1:4,5:9:99:160,0,131
+1	1155757	rs4970422	C	T	42.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.37;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,2:2:6:70,6,0
+1	1156131	rs2887286	T	C	103.03	.	AC=2;AF=1.00;AN=2;DB;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.76;SOR=1.609	GT:AD:DP:GQ:PL	1/1:0,4:4:12:131,12,0
+1	1158631	rs6603781	A	G	376.77	.	AC=2;AF=1.00;AN=2;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.40;SOR=1.445	GT:AD:DP:GQ:PL	1/1:0,12:12:36:405,36,0
+1	1194804	rs11804831	T	C	51.74	.	AC=2;AF=1.00;AN=2;DB;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.87;SOR=2.303	GT:AD:DP:GQ:PL	1/1:0,2:2:6:79,6,0
diff --git a/workflow_lexogen.csv b/workflow_lexogen.csv
index 2c6658d..7f17aa5 100755
--- a/workflow_lexogen.csv
+++ b/workflow_lexogen.csv
@@ -2,6 +2,7 @@ step,protocol,dependencies
 s00_TrimReads,protocols/TrimReads.sh,
 s01_FastQC,protocols/FastQC.sh,s00_TrimReads
 s02_HisatAlignment,protocols/HisatAlignment.sh,s00_TrimReads
+s02_AddOrReplaceReadGroups,protocols/AddOrReplaceReadGroups.sh,s02_HisatAlignment
 s03_MergeBam,protocols/MergeBam.sh,s02_HisatAlignment
 s04_MarkDuplicates,protocols/MarkDuplicates.sh,s03_MergeBam
 s05_QCStats,protocols/QCStats.sh,s04_MarkDuplicates