No false positives in VQSR tranche plot

I'm doing a large variant calling project on a cohort of ~10,000 exomes. I've run into an issue with VQSR. Everything appears to be working normally except for my output tranche plot (attached), where I'm seeing no false positives. I know this is too good to be true.

From reading other posts on here, I used dbsnp_138.b37.excluding_sites_after_129.vcf , but this didn't change my plots. Some other details : my exomes were generated with different kits. While running VQSR I have tried using -L with the superset of all capture regions ( probably not the best idea) and the intersection of all capture regions (what I intend to use), but the tranche plots look the same regardless.

Using GATK v3.5. Any suggestions would be greatly appreciated.

Alex

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Issue · Github
by Sheila

Issue Number
766
State
closed
Last Updated
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Array
Milestone
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Closed By
vdauwera

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @buckleya2
    Hi Alex,

    Can you post the exact command you ran?

    Did you run ApplyRecalibration to generate a final VCF? If so, can you post the command you ran and the VCF header from the output?

    Thanks,
    Sheila

  • Yes I used apply recalibration to make a vcf

    VariantRecalibrator:

    java -Xmx32g -Djava.io.tmpdir=${tmp} -jar ${GATK} \
    -T VariantRecalibrator \
    -R ${ref} \
    -input ${path} \
    -recalFile ${out} \
    -tranchesFile ${out2} \
    -rscriptFile ${filepath}/${short} \
    -nt 6 \
    -tranche 100.0 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranche 90.0 \
    -resource:1000G,known=false,training=true,truth=false,prior=10.0 ${ref_dir}/1000G_phase1.snps.high_confidence.b37.vcf \
    -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ${ref_dir}/dbsnp_138.b37.excluding_sites_after_129.vcf \
    -resource:hapmap,known=false,training=true,truth=true,prior=15.0 ${ref_dir}/hapmap_3.3.b37.sites.vcf \
    -resource:omni,known=false,training=true,truth=true,prior=12.0 ${ref_dir}/1000G_omni2.5.b37.sites.vcf \
    -an QD \
    -an MQ \
    -an MQRankSum \
    -an ReadPosRankSum \
    -an FS \
    -an SOR \
    -an InbreedingCoeff \
    --maxGaussians 6 \
    -mode SNP \
    -L ${exons} \

    ApplyRecalibration:

    java -Xmx32g -Djava.io.tmpdir=${tmp} -jar ${GATK} \
    -T ApplyRecalibration \
    -R ${ref} \
    -input ${path} \
    -recalFile ${recal} \
    -tranchesFile ${tranche} \
    -o ${tmp}/${short}VQSRtest4.rawsnp.vcf \
    -L ${exons} \
    --ts_filter_level 99.5 \
    -mode SNP

    where the recal and tranche files are those generated with VariantRecalibrator and the -L file is a bed file of the common capture regions

    Here is the vcf header :

    fileformat=VCFv4.2

    ALT=<ID=*:DEL,Description="Represents any possible spanning deletion allele at this location">

    ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">

    FILTER=<ID=LowQual,Description="Low quality">

    FILTER=<ID=VQSRTrancheSNP99.50to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -191.7816 <= x < -1.0132">

    FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39998.9886">

    FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39998.9886 <= x < -191.7816">

    FORMAT=<ID=AD,Number=.,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=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">

    FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">

    FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">

    FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

    FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">

    FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">

    GATKCommandLine.ApplyRecalibration=<ID=ApplyRecalibration,Version=3.5-0-g36282e4,Date="Sat Mar 26 19:20:58 PDT 2016",Epoch=1459045258830,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=[/oasis/abuckley/bed/multiintersect.GATK.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/oasis/abuckley/ref/hs37d5.fa 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=/data/tarrango/abuckley/final_vcfs/combined.raw.vcf.gz)] recal_file=(RodBinding name=recal_file source=/oasis/abuckley/megaGG/vcf/combinedVQSRtest4.snp.recal) tranches_file=/oasis/abuckley/megaGG/vcf/combinedVQSRtest4.snp.tranches out=/tmp/combined/combinedVQSRtest4.rawsnp.vcf ts_filter_level=99.5 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.CombineGVCFs=<ID=CombineGVCFs,Version=3.4-0-g7e26428,Date="Thu Feb 18 06:18:04 PST 2016",Epoch=1455805084722,CommandLineOptions="analysis_type=CombineGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/oasis/abuckley/ref/hs37d5.fa 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 out=/oasis/abuckley/megaGG/group.28.gvcf convertToBasePairResolution=false breakBandsAtMultiplesOf=0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.5-0-g36282e4,Date="Tue Feb 23 22:02:54 PST 2016",Epoch=1456293774915,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[1] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/oasis/abuckley/ref/hs37d5.fa 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=6 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 out=/tmp/abuckley/ALL.WXS.1/ALL.WXS.1.raw.vcf 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= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.4-0-g7e26428,Date="Thu Dec 24 12:58:30 PST 2015",Epoch=1450990710829,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/tmp/abuckley/TCGA-XD-AAUH-11A-11D-A40W-08/TCGA-XD-AAUH-11A-11D-A40W-08.S.D.I.B.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=[/cellar/users/abuckley/xml/bed/Agilent_custom.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=100 reference_sequence=/cellar/users/abuckley/ref/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=3 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name=dbsnp source=/cellar/users/abuckley/ref/dbsnp_137.b37.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=false keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)

    GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)

    GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)

    GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)

    GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)

    GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)

    GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)

    GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)

    GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)

    GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)

    GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)

    GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)

    GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)

    GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)

    GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)

    GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)

    GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)

    GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)

    GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)

    GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)

    GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)

    GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)

    GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)

    GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)

    GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)

    GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)

    GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)

    GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)

    GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)

    GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)

    GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)

    GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)

    GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)

    GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)

    GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)

    GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)

    GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)

    GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)

    GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)

    GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)

    GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)

    GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)

    GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)

    GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)

    GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)

    GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)

    GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)

    GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)

    GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)

    GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)

    GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)

    GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)

    GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)

    GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)

    GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)

    GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)

    GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)

    GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)

    GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)

    GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)

    GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)

    GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)

    GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)

    GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)

    GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive)

    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=DB,Number=0,Type=Flag,Description="dbSNP Membership">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

    INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

    INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">

    INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

    INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

    INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">

    INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

    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=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=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">

    INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds 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=1,length=249250621>

    contig=<ID=2,length=243199373>

    contig=<ID=3,length=198022430>

    contig=<ID=4,length=191154276>

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  • Great Thanks! I had a feeling it was related to TsTv but didn't know how.

    I'll try this now and post the new Tranche plot for posterity.

  • Ran again using --target_titv 3. New and improved tranche plot is attached. Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, looks good now! Have fun with your variants.

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