From fc85c751ce3d81a3784d7cef39e9cae872405d08 Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Sun, 17 Oct 2021 11:24:09 -0400
Subject: [PATCH 1/3] Changes for the htsjdk VCFHeader and VCFHeaderLine
 refactoring.

---
 .../picard/fingerprint/FingerprintUtils.java  |   2 +-
 .../java/picard/fingerprint/HaplotypeMap.java |   7 +-
 .../java/picard/vcf/GenotypeConcordance.java  |   4 +-
 ...snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf | 116 +++++++++---------
 ...letionCallset_vs_spanningDeletionTruth.vcf |  17 ++-
 5 files changed, 69 insertions(+), 77 deletions(-)

diff --git a/src/main/java/picard/fingerprint/FingerprintUtils.java b/src/main/java/picard/fingerprint/FingerprintUtils.java
index d1fd5d9a73..51cb2708ce 100644
--- a/src/main/java/picard/fingerprint/FingerprintUtils.java
+++ b/src/main/java/picard/fingerprint/FingerprintUtils.java
@@ -95,7 +95,7 @@ private static VariantContextWriter getVariantContextWriter(final File outputFil
                 .setReferenceDictionary(ref.getSequenceDictionary())
                 .setOutputFile(outputFile).build();
 
-        final Set<VCFHeaderLine> lines = new LinkedHashSet<>();
+        final Set<VCFHeaderLine> lines = VCFHeader.makeHeaderVersionLineSet(VCFHeader.DEFAULT_VCF_VERSION);
         lines.add(new VCFHeaderLine("reference", referenceSequenceFileName.getAbsolutePath()));
         lines.add(new VCFHeaderLine("source", source));
         lines.add(new VCFHeaderLine("fileDate", new Date().toString()));
diff --git a/src/main/java/picard/fingerprint/HaplotypeMap.java b/src/main/java/picard/fingerprint/HaplotypeMap.java
index d323168b43..400690fa24 100644
--- a/src/main/java/picard/fingerprint/HaplotypeMap.java
+++ b/src/main/java/picard/fingerprint/HaplotypeMap.java
@@ -369,12 +369,11 @@ public void writeAsVcf(final File output, final File refFile) throws FileNotFoun
                 .build()) {
 
             final VCFHeader vcfHeader = new VCFHeader(
-                    VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false),
+                    VCFUtils.withUpdatedContigsAsLines(
+                            VCFHeader.makeHeaderVersionLineSet(VCFHeader.DEFAULT_VCF_VERSION),
+                            refFile, header.getSequenceDictionary(), false),
                     Collections.singleton(HET_GENOTYPE_FOR_PHASING));
 
-            VCFUtils.withUpdatedContigsAsLines(Collections.emptySet(), refFile, header.getSequenceDictionary(), false);
-
-            vcfHeader.addMetaDataLine(new VCFHeaderLine(VCFHeaderVersion.VCF4_2.getFormatString(), VCFHeaderVersion.VCF4_2.getVersionString()));
             vcfHeader.addMetaDataLine(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"));
             vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
             vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.String, "Phase-set identifier for phased genotypes."));
diff --git a/src/main/java/picard/vcf/GenotypeConcordance.java b/src/main/java/picard/vcf/GenotypeConcordance.java
index cdbbbcf797..5ab257e399 100644
--- a/src/main/java/picard/vcf/GenotypeConcordance.java
+++ b/src/main/java/picard/vcf/GenotypeConcordance.java
@@ -497,9 +497,7 @@ private Optional<VariantContextWriter> getVariantContextWriter(final VCFFileRead
 
             // create the output header
             final List<String> sampleNames = Arrays.asList(OUTPUT_VCF_CALL_SAMPLE_NAME, OUTPUT_VCF_TRUTH_SAMPLE_NAME);
-            final Set<VCFHeaderLine> headerLines = new HashSet<>();
-            headerLines.addAll(callReader.getFileHeader().getMetaDataInInputOrder());
-            headerLines.addAll(truthReader.getFileHeader().getMetaDataInInputOrder());
+            final Set<VCFHeaderLine> headerLines = VCFHeaderMerger.getMergedHeaderLines(Arrays.asList(callReader.getFileHeader(), truthReader.getFileHeader()), true);
             headerLines.add(CONTINGENCY_STATE_HEADER_LINE);
             writer.writeHeader(new VCFHeader(headerLines, sampleNames));
             return Optional.of(writer);
diff --git a/testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf b/testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf
index 1e80a38ce1..3b677358bf 100644
--- a/testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf
+++ b/testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf
@@ -10,17 +10,13 @@
 ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -38672.7015">
 ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -38672.7015 <= x < -25.4561">
 ##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=DP,Number=1,Type=Integer,Description="Total read depth summed across all datasets, excluding MQ0 reads">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, defined as difference between most likely and next most likely genotype likelihoods">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Net Genotype across all datasets">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods summed across all unfiltered datasets for genotypes as defined in the VCF specification">
 ##FORMAT=<ID=TP,Number=1,Type=Integer,Description="Phred score of the genotype combination and phase given that the genotypes are correct">
-##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.4-33-g9cd2cd4,Date="Wed Jun 24 13:34:15 EDT 2015",Epoch=1435167255521,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[/seq/tng/kbergin/genotype_concordance_tests/NIST_test.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.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=(RodBinding name=variant source=small.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/seq/tng/kbergin/genotype_concordance_tests/NIST.selected.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[QUAL > 10000] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=CombineVariants,Version=3.3-112-g49c8efd,Date="Thu Jan 22 15:25:05 EST 2015",Epoch=1421958305028,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/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=NISTIntegratedCalls_14datasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.18_all_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=true excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version="3.4-33-g9cd2cd4",Date="Wed Jun 24 13:34:15 EDT 2015",Epoch=1435167255521,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[/seq/tng/kbergin/genotype_concordance_tests/NIST_test.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.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=(RodBinding name=variant source=small.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/seq/tng/kbergin/genotype_concordance_tests/NIST.selected.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[QUAL > 10000] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine=<ID=CombineVariants,Version="3.3-112-g49c8efd",Date="Thu Jan 22 15:25:05 EST 2015",Epoch=1421958305028,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/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=NISTIntegratedCalls_14datasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.18_all_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=true excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -89,90 +85,90 @@
 ##PhaseByTransmission="analysis_type=PhaseByTransmission input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[/broad/hptmp/ami/tmp/CEUTrio.ped] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.snps_and_indels.recalibrated.filtered.vcf) DeNovoPrior=1.0E-8 FatherAlleleFirst=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filter_mismatching_base_and_quals=false"
 ##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[/projects/scratch-data-backup/justin.zook/NA12878/bed/union13callableMQonlymerged_addcert_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs_v2.18_2mindatasets_5minYesNoRatio.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/projects/scratch-data-backup/justin.zook/references/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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=LENIENT_VCF_PROCESSING disable_auto_index_creation_and_locking_when_reading_rods=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 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/projects/scratch-data-backup/justin.zook/NA12878/Integration131103/AllFDAdatasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.18_2mindatasets_5minYesNoRatio_all.primitives_nodup.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"
 ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.list] read_buffer_size=null phone_home=NO_ET gatk_key=/humgen/gsa-hpprojects/GATK/data/gatk_user_keys/gsamembers_broadinstitute.org.key read_filter=[] intervals=[/broad/hptmp/ami/tmp/queueScatterGather/.qlog/CEUTrio.indelcall-sg/temp_020_of_300/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=2 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT pcr_error_rate=1.0E-4 noSLOD=false annotateNDA=false min_base_quality_score=17 max_deletion_fraction=0.05 cap_max_alternate_alleles_for_indels=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 dbsnp=(RodBinding name=dbsnp source=/humgen/gsa-hpprojects/GATK/bundle/current/b37/dbsnp_135.b37.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
-##contig=<ID=1,length=249250621>
+##contig=<ID=1,length=249250621,assembly=b37>
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diff --git a/testdata/picard/vcf/spanningDeletionCallset_vs_spanningDeletionTruth.vcf b/testdata/picard/vcf/spanningDeletionCallset_vs_spanningDeletionTruth.vcf
index 31f9b677ce..54bdc326cb 100644
--- a/testdata/picard/vcf/spanningDeletionCallset_vs_spanningDeletionTruth.vcf
+++ b/testdata/picard/vcf/spanningDeletionCallset_vs_spanningDeletionTruth.vcf
@@ -24,15 +24,14 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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-##GATKCommandLine.ApplyRecalibration.3=<ID=ApplyRecalibration,Version=3.7-1-g48c2a01,Date="Sun Jan 01 22:34:52 EST 2017",Epoch=1483328092995,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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 input=[(RodBinding name=input source=LCRTest.filtered.original.vcf.gz)] recal_file=(RodBinding name=recal_file source=LCRTest_recalibrate_SNP_onChrX.recal) tranches_file=LCRTest_recalibrate_SNP_onChrX.tranche out=/humgen/gsa-hpprojects/dev/pjfan/VQSR_XChrom_Exploration/LCRInvestigationWGSdatasetFromMshand_chrX/LCRTest.filtered.original.onChrX.SNPfiltered.vcf ts_filter_level=99.0 useAlleleSpecificAnnotations=false lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.ApplyRecalibration.4=<ID=ApplyRecalibration,Version=3.7-1-g48c2a01,Date="Sun Jan 01 22:56:33 EST 2017",Epoch=1483329393893,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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 input=[(RodBinding name=input source=LCRTest.filtered.original.onChrX.SNPfiltered.vcf)] recal_file=(RodBinding name=recal_file source=LCRTest_recalibrate_INDEL_onChrX.recal) tranches_file=LCRTest_recalibrate_INDEL_onChrX.tranche out=/humgen/gsa-hpprojects/dev/pjfan/VQSR_XChrom_Exploration/LCRInvestigationWGSdatasetFromMshand_chrX/LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.vcf ts_filter_level=99.0 useAlleleSpecificAnnotations=false lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,Version=3.5-0-g36282e4,Date="Fri May 27 01:37:13 UTC 2016",Epoch=1464313033521,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-0/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input2 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-1/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input3 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-2/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input4 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-3/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input5 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-4/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input6 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-5/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input7 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-6/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input8 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-7/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input9 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-8/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input10 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-9/LCRTest.variant_filtered.vcf.gz)] recal_file=(RodBinding name=recal_file source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-IndelsVariantRecalibratorOriginalAfter/LCRTest.indels.recal) tranches_file=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-IndelsVariantRecalibratorOriginalAfter/LCRTest.indels.tranches out=/cromwell_root/LCRTest.tmp_indel_filtered.vcf.gz ts_filter_level=99.7 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.5-0-g36282e4,Date="Thu May 26 17:46:03 UTC 2016",Epoch=1464284763127,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=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-TileDBCombineGVCF/shard-9/output.vcf.gz)])] out=/cromwell_root/LCRTest.unfiltered.vcf.gz includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[] group=[Standard] dbsnp=(RodBinding name=dbsnp source=broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.SelectVariants.2=<ID=SelectVariants,Version=3.7-13-geeb6d9c,Date="Wed Feb 01 14:05:02 EST 2017",Epoch=1485975902482,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[chrX] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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=(RodBinding name=variant source=LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.OnlyX.OnlyCHMI_CHMI3_WGS2.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/dsde/working/fleharty/forPeter/chrXCallset.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-13-geeb6d9c,Date="Thu Jan 19 10:27:56 EST 2017",Epoch=1484839676153,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[chrX] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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=(RodBinding name=variant source=LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/humgen/gsa-hpprojects/dev/pjfan/VQSR_XChrom_Exploration/LCRInvestigationWGSdatasetFromMshand_chrX/LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.OnlyX.OnlyCHMI_CHMI3_WGS2.vcf sample_name=[CHMI_CHMI3_WGS2] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=true excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-13-geeb6d9c,Date="Wed Feb 01 14:06:17 EST 2017",Epoch=1485975977776,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[chrX] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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=(RodBinding name=variant source=h2.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/dsde/working/fleharty/forPeter/chrXTruth.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.5-0-g36282e4,Date="Fri May 27 00:22:26 UTC 2016",Epoch=1464308546074,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-TabixAndGenotypeGVCF/shard-2/LCRTest.unfiltered.vcf.gz) mask=(RodBinding name= source=UNBOUND) out=/cromwell_root/LCRTest.variant_filtered.vcf.gz filterExpression=[vc.hasAttribute("ExcessHet") && vc.getAttribute("ExcessHet") > 54.69] filterName=[ExcessHet] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.ApplyRecalibration.2=<ID=ApplyRecalibration,Version="3.5-0-g36282e4",Date="Fri May 27 02:40:41 UTC 2016",Epoch=1464316841882,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-IndelsApplyRecalibrationOriginalAfter/LCRTest.tmp_indel_filtered.vcf.gz)] recal_file=(RodBinding name=recal_file source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-SNPSVariantRecalibratorOriginalAfter/LCRTest.snps.recal) tranches_file=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-SNPSVariantRecalibratorOriginalAfter/LCRTest.snps.tranches out=/cromwell_root/LCRTest.filtered.original.vcf.gz ts_filter_level=99.7 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.ApplyRecalibration.3=<ID=ApplyRecalibration,Version="3.7-1-g48c2a01",Date="Sun Jan 01 22:34:52 EST 2017",Epoch=1483328092995,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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 input=[(RodBinding name=input source=LCRTest.filtered.original.vcf.gz)] recal_file=(RodBinding name=recal_file source=LCRTest_recalibrate_SNP_onChrX.recal) tranches_file=LCRTest_recalibrate_SNP_onChrX.tranche out=/humgen/gsa-hpprojects/dev/pjfan/VQSR_XChrom_Exploration/LCRInvestigationWGSdatasetFromMshand_chrX/LCRTest.filtered.original.onChrX.SNPfiltered.vcf ts_filter_level=99.0 useAlleleSpecificAnnotations=false lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.ApplyRecalibration.4=<ID=ApplyRecalibration,Version="3.7-1-g48c2a01",Date="Sun Jan 01 22:56:33 EST 2017",Epoch=1483329393893,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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 input=[(RodBinding name=input source=LCRTest.filtered.original.onChrX.SNPfiltered.vcf)] recal_file=(RodBinding name=recal_file source=LCRTest_recalibrate_INDEL_onChrX.recal) tranches_file=LCRTest_recalibrate_INDEL_onChrX.tranche out=/humgen/gsa-hpprojects/dev/pjfan/VQSR_XChrom_Exploration/LCRInvestigationWGSdatasetFromMshand_chrX/LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.vcf ts_filter_level=99.0 useAlleleSpecificAnnotations=false lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,Version="3.5-0-g36282e4",Date="Fri May 27 01:37:13 UTC 2016",Epoch=1464313033521,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-0/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input2 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-1/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input3 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-2/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input4 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-3/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input5 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-4/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input6 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-5/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input7 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-6/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input8 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-7/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input9 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-8/LCRTest.variant_filtered.vcf.gz), (RodBinding name=input10 source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-VariantFiltrationExcessHet/shard-9/LCRTest.variant_filtered.vcf.gz)] recal_file=(RodBinding name=recal_file source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-IndelsVariantRecalibratorOriginalAfter/LCRTest.indels.recal) tranches_file=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-IndelsVariantRecalibratorOriginalAfter/LCRTest.indels.tranches out=/cromwell_root/LCRTest.tmp_indel_filtered.vcf.gz ts_filter_level=99.7 lodCutoff=null ignore_filter=null ignore_all_filters=false excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version="3.5-0-g36282e4",Date="Thu May 26 17:46:03 UTC 2016",Epoch=1464284763127,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=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-TileDBCombineGVCF/shard-9/output.vcf.gz)])] out=/cromwell_root/LCRTest.unfiltered.vcf.gz includeNonVariantSites=false uniquifySamples=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[] group=[Standard] dbsnp=(RodBinding name=dbsnp source=broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.SelectVariants.2=<ID=SelectVariants,Version="3.7-13-geeb6d9c",Date="Wed Feb 01 14:05:02 EST 2017",Epoch=1485975902482,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[chrX] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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=(RodBinding name=variant source=LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.OnlyX.OnlyCHMI_CHMI3_WGS2.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/dsde/working/fleharty/forPeter/chrXCallset.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version="3.7-13-geeb6d9c",Date="Thu Jan 19 10:27:56 EST 2017",Epoch=1484839676153,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[chrX] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/seq/references/Homo_sapiens_assembly38/v0/Homo_sapiens_assembly38.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 secondsBetweenProgressUpdates=10 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=(RodBinding name=variant source=LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/humgen/gsa-hpprojects/dev/pjfan/VQSR_XChrom_Exploration/LCRInvestigationWGSdatasetFromMshand_chrX/LCRTest.filtered.original.onChrX.SNPfiltered.INDELfiltered.OnlyX.OnlyCHMI_CHMI3_WGS2.vcf sample_name=[CHMI_CHMI3_WGS2] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=true excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version="3.5-0-g36282e4",Date="Fri May 27 00:22:26 UTC 2016",Epoch=1464308546074,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[broad-references/hg38/v0/wgs_calling_regions.v1.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=broad-references/hg38/v0/Homo_sapiens_assembly38.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 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=broad-gotc-dev-storage/cromwell_execution/FilterLCRJointGenotyping/cfe3f689-120f-4a76-b906-2204df6f2c57/call-TabixAndGenotypeGVCF/shard-2/LCRTest.unfiltered.vcf.gz) mask=(RodBinding name= source=UNBOUND) out=/cromwell_root/LCRTest.variant_filtered.vcf.gz filterExpression=[vc.hasAttribute(ExcessHet) && vc.getAttribute(ExcessHet) > 54.69] filterName=[ExcessHet] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

From b38406afa3c894f5ed6e39ac74c125fb74afb559 Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Wed, 17 May 2023 12:45:22 -0400
Subject: [PATCH 2/3] Update header merging.

---
 src/main/java/picard/vcf/GenotypeConcordance.java | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/main/java/picard/vcf/GenotypeConcordance.java b/src/main/java/picard/vcf/GenotypeConcordance.java
index 5ab257e399..4d66851eb3 100644
--- a/src/main/java/picard/vcf/GenotypeConcordance.java
+++ b/src/main/java/picard/vcf/GenotypeConcordance.java
@@ -40,13 +40,7 @@
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
-import htsjdk.variant.vcf.VCFConstants;
-import htsjdk.variant.vcf.VCFFileReader;
-import htsjdk.variant.vcf.VCFHeader;
-import htsjdk.variant.vcf.VCFHeaderLine;
-import htsjdk.variant.vcf.VCFHeaderLineCount;
-import htsjdk.variant.vcf.VCFHeaderLineType;
-import htsjdk.variant.vcf.VCFInfoHeaderLine;
+import htsjdk.variant.vcf.*;
 import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
 import org.broadinstitute.barclay.help.DocumentedFeature;

From 2c4f23219e640ad0d90d135e3c6af263542ad19a Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Wed, 17 May 2023 12:45:40 -0400
Subject: [PATCH 3/3] Temporarily use htsjdk snapshot.

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 0d7259299b..f4bb26eca4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -57,7 +57,7 @@ def ensureBuildPrerequisites(buildPrerequisitesMessage) {
 
 ensureBuildPrerequisites(buildPrerequisitesMessage)
 
-final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.1')
+final htsjdkVersion = System.getProperty('htsjdk.version', '3.0.5-12-g5700958-SNAPSHOT')
 final googleNio = 'com.google.cloud:google-cloud-nio:0.123.25'
 
 configurations {