From cb099242df2d6d469f59c422ff21ee92f8724cf4 Mon Sep 17 00:00:00 2001
From: Orli Cohen <ocohen@broadinstitute.org>
Date: Wed, 29 Jun 2022 21:31:09 -0400
Subject: [PATCH] responding to review

---
 .../walkers/variantutils/VariantsToTable.java |   2 +-
 .../VariantsToTableIntegrationTest.java       |   4 +-
 .../VariantsToTable/1000G.phase3.snippet.vcf  |  48 -------
 .../expected.noFieldsSpecified.table          |   4 -
 ...raheaderlinesdeleted_dbsnp_138.snippet.vcf | 117 ------------------
 5 files changed, 3 insertions(+), 172 deletions(-)
 delete mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf
 delete mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/expected.noFieldsSpecified.table
 delete mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/extraheaderlinesdeleted_dbsnp_138.snippet.vcf

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java
index 83fe33d671d..db5d4e2e63c 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable.java
@@ -246,7 +246,7 @@ public void onTraversalStart() {
 
         // if fields specified, but none are genotype fields, set samples to empty
         if (genotypeFieldsToTake.isEmpty() && asGenotypeFieldsToTake.isEmpty()) {
-                samples = Collections.emptySortedSet();
+            samples = Collections.emptySortedSet();
         }
         else {
             final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
index f7426201709..10c922a267a 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTableIntegrationTest.java
@@ -239,10 +239,10 @@ public void testMoltenOutputWithMultipleAlleles() throws IOException {
     }
 
     @Test
-    public void testNoFieldsSpecified() throws IOException {
+    public void testNoFieldsSpecifiedNoSamples() throws IOException {
         final File inputFile = new File(getToolTestDataDir(), "VCFWithoutGenotypes_dbsnp_138.snippet.vcf");
         final File outputFile = createTempFile("noFieldsSpecifiedOutput", ".table");
-        final File expectedFile = new File(getToolTestDataDir(), "expected.noFieldsSpecified.table");
+        final File expectedFile = new File(getToolTestDataDir(), "expected.noFieldsSpecifiedNoSamples.table");
 
         final String[] args = new String[] {"--variant", inputFile.getAbsolutePath(),
                 "-O", outputFile.getAbsolutePath()};
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf
deleted file mode 100644
index eaf1060e2e7..00000000000
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf
+++ /dev/null
@@ -1,48 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=VQSRTrancheINDEL99.00to99.50,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1.0597 <= x < 0.1687">
-##FILTER=<ID=VQSRTrancheINDEL99.50to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -5.8589 <= x < -1.0597">
-##FILTER=<ID=VQSRTrancheINDEL99.90to99.95,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -6.5565 <= x < -5.8589">
-##FILTER=<ID=VQSRTrancheINDEL99.95to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -70.77">
-##FILTER=<ID=VQSRTrancheINDEL99.95to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -70.77 <= x < -6.5565">
-##FILTER=<ID=VQSRTrancheSNP99.90to99.95,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -96.2455 <= x < -14.2763">
-##FILTER=<ID=VQSRTrancheSNP99.95to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -437.9355">
-##FILTER=<ID=VQSRTrancheSNP99.95to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -437.9355 <= x < -96.2455">
-##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">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##GATKCommandLine=<ID=ApplyRecalibration,Version=2.6-20-g0728857,Date="Mon Jul 01 11:58:36 EDT 2013",Epoch=1372694316825,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[20] 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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=5 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 input=[(RodBinding name=input source=/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.lowpass.hc.recal.vcf)] recal_file=(RodBinding name=recal_file source=/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.lowpass.hc.recal.recal) tranches_file=/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.lowpass.hc.recal.tranches 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 ts_filter_level=99.0 ignore_filter=null mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/1000G.phase3.snippet.vcf --sample-name HG00096 --sample-name HG00097 --sample-name HG00099 --variant src/test/resources/large/1000G.phase3.broad.withGenotypes.chr20.10100000.vcf --intervals 20:10000054-10000117 --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.2.6.1-22-gd4f083d-SNAPSHOT",Date="June 21, 2022 1:46:50 PM EDT">
-##GATKVersion=2.5-191-g02f8427
-##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[/humgen/1kg/processing/production_wgs_final/chr20/ALL.chr20.bam.list] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/humgen/1kg/processing/production_wgs_final/chr20/.queue/scatterGather/call.for.1000G-1-sg/temp_0001_of_1000/scatter.intervals] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/1kg/reference/human_g1k_v37_decoy.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=200 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=null 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 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 graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name= source=UNBOUND) comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.05 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null useDebruijnAssembler=false minKmerForDebruijnAssembler=11 onlyUseKmerSizeForDebruijnAssembler=-1 kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false numPruningSamples=3 maxPathsPerSample=8 dontRecoverDanglingTails=false minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false useFilteredReadsForAnnotations=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=25 mergeVariantsViaLD=false pair_hmm_implementation=LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debug=false debugGraphTransformations=false useLowQualityBasesForAssembly=false dontTrimActiveRegions=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 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">
-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
-##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=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">
-##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
-##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
-##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
-##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
-##contig=<ID=20,length=63025520>
-##contig=<ID=21,length=48129895>
-##source=SelectVariants
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00097	HG00099
-20	10000054	.	CTTTG	C	504.42	PASS	AC=0;AF=0.00;AN=6;BaseQRankSum=-0.975;ClippingRankSum=-2.925;DP=22;FS=1.899;InbreedingCoeff=0.0592;MQ=59.27;MQ0=0;MQRankSum=-3.212;QD=2.43;ReadPosRankSum=-0.264;VQSLOD=5.10;culprit=FS	GT:AD:DP:GQ:PL	0/0:2,0:2:6:0,6,119	0/0:10,0:10:29:0,29,592	0/0:10,0:10:30:0,30,598
-20	10000107	.	T	C	263.95	PASS	AC=0;AF=0.00;AN=6;BaseQRankSum=-0.444;ClippingRankSum=-3.132;DP=25;FS=0.948;InbreedingCoeff=-0.0102;MQ=59.19;MQ0=0;MQRankSum=2.292;POSITIVE_TRAIN_SITE;QD=10.56;ReadPosRankSum=0.055;VQSLOD=7.76;culprit=FS	GT:AD:DP:GQ:PL	0/0:5,0:5:15:0,15,387	0/0:13,0:13:42:0,42,786	0/0:7,0:7:24:0,24,548
-20	10000117	.	C	T	329458.17	PASS	AC=1;AF=0.167;AN=6;BaseQRankSum=10.505;ClippingRankSum=-20.658;DP=28;FS=8.305;InbreedingCoeff=0.1727;MQ=59.17;MQ0=0;MQRankSum=2.689;POSITIVE_TRAIN_SITE;QD=25.46;ReadPosRankSum=-4.688;VQSLOD=3.19;culprit=ReadPosRankSum	GT:AD:DP:GQ:PL	0/0:5,0:5:15:0,15,189	0/1:8,8:16:99:254,0,231	0/0:7,0:7:21:0,21,271
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/expected.noFieldsSpecified.table b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/expected.noFieldsSpecified.table
deleted file mode 100644
index 6a6253c3ca6..00000000000
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/expected.noFieldsSpecified.table
+++ /dev/null
@@ -1,4 +0,0 @@
-CHROM	POS	ID	REF	ALT	QUAL	FILTER	AC	CAF	CLNDSDB	COMMON	DP	DSS	HD	KGPROD	KGPhase1	LSD	REF	RS	RSPOS	SAO	SSR	VC	VP	WGT	dbSNPBuildID
-20	10000092	rs183046704	T	G	-10.0	PASS	NA	[0.9991,0.0009183]	NA	0	NA	NA	NA	true	true	NA	T	183046704	10000092	0	0	SNV	0x050000000001000014000100	1	135
-20	10000107	rs188245245	T	C	-10.0	PASS	NA	[0.9982,0.001837]	NA	0	NA	NA	NA	true	true	NA	T	188245245	10000107	0	0	SNV	0x050000000001000014000100	1	135
-20	10000117	rs4816203	C	T	-10.0	PASS	NA	[0.3682,0.6318]	NA	1	NA	NA	NA	true	true	NA	C	4816203	10000117	0	0	SNV	0x05010000000117011e000100	1	111
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/extraheaderlinesdeleted_dbsnp_138.snippet.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/extraheaderlinesdeleted_dbsnp_138.snippet.vcf
deleted file mode 100644
index 628a1d05d1e..00000000000
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/extraheaderlinesdeleted_dbsnp_138.snippet.vcf
+++ /dev/null
@@ -1,117 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=NC,Description="Inconsistent Genotype Submission For At Least One Sample">
-##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.4-46-gbc02625,Date="Wed Aug 19 10:29:53 EDT 2015",Epoch=1439994593766,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=[20:10000000-10250000, 21:10000000-10250000] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=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=(RodBinding name=variant source=dbsnp_138.b37.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/home/unix/droazen/bundle_snippets/dbsnp_138.b37.20.21.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 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=LeftAlignAndTrimVariants,Version=2.7-63-g8d09086,Date="Mon Nov 04 10:02:23 EST 2013",Epoch=1383577343781,CommandLineOptions="analysis_type=LeftAlignAndTrimVariants input_file=[] 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 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 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false 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 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=138/00-All.vcf) trimAlleles=false splitMultiallelics=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_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
-##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/VariantsToTable/dbsnp_138.snippet.vcf --variant src/test/resources/large/dbsnp_138.b37.20.21.vcf --intervals 20:10000092-10000117 --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --genomicsdb-max-alternate-alleles 50 --call-genotypes false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.2.6.1-22-gd4f083d-SNAPSHOT",Date="June 21, 2022 1:56:58 PM EDT">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column.  The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF.  This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
-##INFO=<ID=CLNDSDB,Number=.,Type=String,Description="Variant disease database name">
-##INFO=<ID=COMMON,Number=1,Type=Integer,Description="RS is a common SNP.  A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency.">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75">
-##INFO=<ID=HD,Number=0,Type=Flag,Description="Marker is on high density genotyping kit (50K density or greater).  The variant may have phenotype associations present in dbGaP.">
-##INFO=<ID=KGPROD,Number=0,Type=Flag,Description="Has 1000 Genome submission">
-##INFO=<ID=KGPhase1,Number=0,Type=Flag,Description="1000 Genome phase 1 (incl. June Interim phase 1)">
-##INFO=<ID=LSD,Number=0,Type=Flag,Description="Submitted from a locus-specific database">
-##INFO=<ID=REF,Number=0,Type=Flag,Description="Has reference A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8">
-##INFO=<ID=RS,Number=1,Type=Integer,Description="dbSNP ID (i.e. rs number)">
-##INFO=<ID=RSPOS,Number=1,Type=Integer,Description="Chr position reported in dbSNP">
-##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
-##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
-##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
-##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property.  Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf">
-##INFO=<ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
-##INFO=<ID=dbSNPBuildID,Number=1,Type=Integer,Description="First dbSNP Build for RS">
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-##dbSNP_BUILD_ID=138
-##fileDate=20130806
-##phasing=partial
-##source=SelectVariants
-##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf	
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-20	10000092	rs183046704	T	G	.	.	CAF=[0.9991,0.0009183];COMMON=0;KGPROD;KGPhase1;RS=183046704;RSPOS=10000092;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000014000100;WGT=1;dbSNPBuildID=135
-20	10000107	rs188245245	T	C	.	.	CAF=[0.9982,0.001837];COMMON=0;KGPROD;KGPhase1;RS=188245245;RSPOS=10000107;SAO=0;SSR=0;VC=SNV;VP=0x050000000001000014000100;WGT=1;dbSNPBuildID=135
-20	10000117	rs4816203	C	T	.	.	CAF=[0.3682,0.6318];COMMON=1;G5;G5A;GNO;KGPROD;KGPhase1;KGPilot123;OTHERKG;RS=4816203;RSPOS=10000117;SAO=0;SLO;SSR=0;VC=SNV;VLD;VP=0x05010000000117011e000100;WGT=1;dbSNPBuildID=111