string length error generated by funcotator while processing a mutect2 vcf
A string length error is generated by functator while processing a vcf from mutect2.
java.lang.StringIndexOutOfBoundsException: begin 1086, end 1089, length 1086 (more below)
funcotator stops at exactly the same place in chr12 in both the unfiltered and filtered vcf.
Checked the subsequent (and prior) line lengths and there are no lines in the vcf that are near to the 1000 characters. Not obvious what to look for in the format strings to find/fix the culprit?
REQUIRED for all errors and issues:
a) GATK version used:
docker broadinstitute/gatk:latest
The Genome Analysis Toolkit (GATK) v4.4.0.0
HTSJDK Version: 3.0.5
Picard Version: 3.0.0
b) Exact command used: (essentially the default)
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --normal-sample NSCLC_11111-1dbf7_DN_BoldQuail --output mydata/NSCLC_11111_BoldQuail/analysis/NSCLC_11111-e9ac3_RT_BoldQuail_mutect2_STAR-cigarsplit-transcriptome_unfiltered_hg38.vcf --intervals mydata/refs/hg38_exons.interval_list --interval-padding 32 --input mydata/NSCLC_11111_BoldQuail/bsqr/NSCLC_11111-e9ac3_RT_BoldQuail_Aligned.sortedByCoord.cigarsplit.bam --input mydata/NSCLC_11111_BoldQuail/bsqr/NSCLC_11111-1dbf7_DN_BoldQuail_Nbwa_dedup_bsqr_hg38.bam --reference mydata/refs/Homo_sapiens_assembly38.fasta --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --flow-use-t0-tag false --flow-probability-threshold 0.003 --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --flow-number-of-uncertain-flows-to-clip 0 --flow-nucleotide-of-first-uncertain-flow T --keep-boundary-flows false --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --mutect3-training-mode false --mutect3-ref-downsample 10 --mutect3-alt-downsample 20 --mutect3-non-artifact-ratio 20 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --flow-mode NONE --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --pileup-detection-enable-indel-pileup-calling false --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.5 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --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 --minimum-mapping-quality 20 --max-read-length 2147483647 --min-read-length 30 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.4.0.0",Date="October 1, 2023 at 10:10:05 PM GMT">
##MutectVersion=2.2 (docker version)
##fileformat=VCFv4.2
c) Entire program log:
this is the error log when funcotator stopped processing the vcf
[October 11, 2023 at 5:19:35 AM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 159.82 minutes.
Runtime.totalMemory()=7667187712
java.lang.StringIndexOutOfBoundsException: begin 1086, end 1089, length 1086
at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4602)
at java.base/java.lang.String.substring(String.java:2705)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.getCodonChangeStringForFrameShifts(FuncotatorUtils.java:811)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.getCodonChangeString(FuncotatorUtils.java:646)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createCodingRegionFuncotationForProteinCodingFeature(GencodeFuncotationFactory.java:1269)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createExonFuncotation(GencodeFuncotationFactory.java:1083)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationOnSingleTranscript(GencodeFuncotationFactory.java:1020)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:847)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsHelper(GencodeFuncotationFactory.java:831)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.lambda$createGencodeFuncotationsByAllTranscripts$0(GencodeFuncotationFactory.java:508)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createGencodeFuncotationsByAllTranscripts(GencodeFuncotationFactory.java:509)
at org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotationFactory.createFuncotationsOnVariant(GencodeFuncotationFactory.java:564)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.determineFuncotations(DataSourceFuncotationFactory.java:243)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:211)
at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:182)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.lambda$createFuncotationMapForVariant$0(FuncotatorEngine.java:152)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:162)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:924)
at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:878)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
-
Can you post the problematic VCF line here so that we may be able to test it better?
Can you also make sure that you are using the compatible versions of Funcotator resource and GATK. (1.7 and 4.4.0.0 or 4.3.0.0)
-
The problem is that I can not figure out what line is the problem. chr12 98601528 is the last line in the funcotator .maf. Funcotator seems to grab a number of lines at a time while it is working and so I don't know whether the next line chr12 98601534 is the problem or not. I am attaching a hundred lines of the vcf below.
I presume that the :latest docker files posted at the docker hub repository are compatible?!!
I am using the funcotator resources 1.7.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NSCLC_11111-1dbf7_DN_BoldQuail NSCLC_11111_BoldQuail
chr12 98601528 . G T,GT . clustered_events;multiallelic;normal_artifact AS_FilterStatus=SITE|strand_bias;AS_SB_TABLE=840,1868|6,23|1,14;DP=2855;ECNT=57;GERMQ=93;MBQ=37,37,37;MFRL=0,0,0;MMQ=60,60,60;MPOS=69,28;NALOD=1.08,1.14;NLOD=11.88,11.77;POPAF=6.00,6.00;TLOD=31.43,16.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:42,1,1:0.030,0.024:44:18,1,1:20,0,0:42,1,1:13,29,0,2 0/1/2:2666,28,14:7.049e-03,6.395e-03:2708:852,7,12:819,4,1:2238,29,14:827,1839,7,35
chr12 98601534 . TCAAAG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=775,1886|0,14;DP=2782;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=51;NALOD=1.61;NLOD=11.38;POPAF=6.00;TLOD=6.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:38,0:0.024:38:15,0:17,0:38,0:9,29,0,0 0/1:2623,14:5.929e-03:2637:854,2:768,0:2219,14:766,1857,0,14
chr12 98601535 . CAA C,CA . clustered_events;multiallelic;strand_bias AS_FilterStatus=strand_bias|strand_bias;AS_SB_TABLE=772,1884|0,6|0,10;DP=2756;ECNT=57;GERMQ=93;MBQ=37,37,37;MFRL=0,0,0;MMQ=60,60,60;MPOS=74,56;NALOD=1.17,1.15;NLOD=12.34,11.42;POPAF=6.00,6.00;RPA=3,1,2;RU=A;STR;STRQ=93;TLOD=6.84,5.65 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:38,0,0:0.023,0.024:38:15,0,0:15,0,0:38,0,0:9,29,0,0 0/1/2:2618,6,10:3.013e-03,4.628e-03:2634:847,4,6:737,0,1:2208,6,10:763,1855,0,16
chr12 98601536 . AAAGC A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=758,1895|2,12;DP=2738;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=52;NALOD=1.32;NLOD=11.38;POPAF=6.00;TLOD=7.44 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:38,0:0.024:38:15,0:17,0:38,0:9,29,0,0 0/1:2615,14:1.421e-03:2629:845,0:744,2:2200,12:749,1866,2,12
chr12 98601538 . AG A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=737,1872|5,9;DP=2694;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=53;NALOD=1.31;NLOD=11.25;POPAF=6.00;TLOD=22.74 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:38,0:0.025:38:16,0:18,0:38,0:9,29,0,0 0/1:2571,14:2.751e-03:2585:853,2:715,5:2183,9:728,1843,5,9
chr12 98601539 . G C,T . clustered_events;multiallelic;strand_bias AS_FilterStatus=strand_bias|strand_bias;AS_SB_TABLE=732,1840|0,6|1,19;DP=2667;ECNT=57;GERMQ=93;MBQ=37,37,37;MFRL=0,0,0;MMQ=60,60,60;MPOS=74,59;NALOD=1.15,1.14;NLOD=11.74,11.10;POPAF=6.00,6.00;TLOD=6.93,33.15 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:37,0,0:0.024,0.024:37:15,0,0:18,0,0:37,0,0:9,28,0,0 0/1/2:2535,6,20:3.129e-03,9.169e-03:2561:843,4,11:690,0,1:2150,6,20:723,1812,1,25
chr12 98601545 . GT G . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=642,1821|3,3;DP=2560;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=48;NALOD=1.54;NLOD=9.87;POPAF=6.00;TLOD=11.78 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:33,0:0.028:33:14,0:15,0:33,0:7,26,0,0 0/1:2430,6:1.916e-03:2436:804,0:620,3:2077,3:635,1795,3,3
chr12 98601546 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=613,1699|13,17;DP=2556;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=55;NALOD=1.08;NLOD=9.51;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=46.89 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:32,0:0.029:32:14,0:14,0:32,0:6,26,0,0 0/1:2280,30:0.012:2310:768,7:581,14:1926,26:607,1673,13,17
chr12 98601551 . T A . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=582,1759|0,6;DP=2347;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=4;NALOD=1.51;NLOD=9.33;POPAF=6.00;TLOD=6.82 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:31,0:0.030:31:14,0:13,0:31,0:0|1:98601551_T_A:98601551:6,25,0,0 0|1:2310,6:3.531e-03:2316:741,5:516,0:1958,6:0|1:98601551_T_A:98601551:576,1734,0,6
chr12 98601553 . A T . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=523,1627|0,6;DP=2156;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=2;NALOD=1.51;NLOD=9.33;POPAF=6.00;TLOD=7.08 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:31,0:0.030:31:14,0:13,0:31,0:0|1:98601551_T_A:98601551:6,25,0,0 0|1:2119,6:3.850e-03:2125:738,5:479,0:1796,6:0|1:98601551_T_A:98601551:517,1602,0,6
chr12 98601555 . TCTG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=458,1547|6,11;DP=2117;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=28;NALOD=1.50;NLOD=9.03;POPAF=6.00;TLOD=22.60 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:30,0:0.031:30:13,0:13,0:30,0:6,24,0,0 0/1:1975,17:5.045e-03:1992:729,3:469,6:1697,9:452,1523,6,11
chr12 98601556 . C T . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=478,1538|3,11;DP=2085;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=25;NALOD=1.20;NLOD=9.02;POPAF=6.00;TLOD=23.20 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:30,0:0.031:30:14,0:13,0:30,0:5,25,0,0 0/1:1986,14:6.850e-03:2000:712,8:457,3:1697,11:473,1513,3,11
chr12 98601557 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=451,1536|6,13;DP=2098;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=39;NALOD=1.20;NLOD=8.70;POPAF=6.00;TLOD=32.88 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:29,0:0.032:29:13,0:13,0:29,0:5,24,0,0 0/1:1958,19:8.683e-03:1977:714,6:450,6:1688,14:446,1512,6,13
chr12 98601558 . G C . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=438,1519|14,21;DP=2053;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=16;NALOD=1.20;NLOD=8.72;POPAF=6.00;TLOD=51.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:29,0:0.032:29:13,0:13,0:29,0:5,24,0,0 0/1:1928,35:7.765e-03:1963:713,2:426,10:1669,23:433,1495,14,21
chr12 98601574 . T G . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=303,1374|0,8;DP=1686;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=7;NALOD=1.49;NLOD=9.03;POPAF=6.00;TLOD=5.23 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:30,0:0.031:30:11,0:13,0:30,0:4,26,0,0 0/1:1647,8:6.053e-03:1655:624,8:253,0:1423,8:299,1348,0,8
chr12 98601577 . AG A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=241,1305|4,9;DP=1601;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=25;NALOD=1.44;NLOD=7.97;POPAF=6.00;TLOD=12.81 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:27,0:0.035:27:11,0:13,0:27,0:3,24,0,0 0/1:1519,13:5.001e-03:1532:616,1:236,4:1349,6:238,1281,4,9
chr12 98601578 . G A . clustered_events;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=240,1290|4,29;DP=1598;ECNT=57;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=25;NALOD=0.027;NLOD=4.85;POPAF=6.00;TLOD=22.19 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:25,1:0.071:26:10,1:12,0:25,1:3,22,0,1 0/1:1505,32:0.015:1537:608,15:223,0:1338,25:237,1268,4,28
chr12 98613610 . AT A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=13,14|2,2;DP=31;ECNT=1;GERMQ=92;MBQ=20,37;MFRL=207,0;MMQ=60,60;MPOS=61;NALOD=1.40;NLOD=7.10;POPAF=6.00;RPA=3,2;RU=T;STR;STRQ=93;TLOD=13.81 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:27,0:0.039:27:9,0:14,0:24,0:13,14,0,0 0/1:0,4:0.750:4:0,0:0,2:0,2:0,0,2,2
chr12 98614101 . T C . strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=131,94|21,0;DP=250;ECNT=1;GERMQ=93;MBQ=20,37;MFRL=175,0;MMQ=60,60;MPOS=7;NALOD=2.12;NLOD=38.47;POPAF=6.00;TLOD=69.91 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:186,0:7.628e-03:186:62,0:64,0:128,0:92,94,0,0 0/1:39,21:0.355:60:0,0:39,21:39,21:39,0,21,0
chr12 98614159 . C CT . PASS AS_FilterStatus=SITE;AS_SB_TABLE=143,28|21,0;DP=201;ECNT=2;GERMQ=93;MBQ=34,37;MFRL=144,0;MMQ=60,60;MPOS=65;NALOD=2.02;NLOD=28.81;POPAF=6.00;RPA=3,4;RU=T;STR;STRQ=93;TLOD=48.57 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:103,0:9.561e-03:103:46,0:45,0:99,0:76,27,0,0 0/1:68,21:0.244:89:0,0:67,21:67,21:67,1,21,0
chr12 98614220 . GT G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=73,105|21,21;DP=230;ECNT=2;GERMQ=93;MBQ=36,37;MFRL=0,0;MMQ=60,60;MPOS=18;NALOD=1.97;NLOD=25.17;POPAF=6.00;RPA=5,4;RU=T;STR;STRQ=93;TLOD=115.02 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:94,0:0.011:94:44,0:26,0:87,0:24,70,0,0 0/1:84,42:0.239:126:10,0:48,21:69,21:49,35,21,21
chr12 98625944 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=12,7|4,0;DP=24;ECNT=1;GERMQ=61;MBQ=20,37;MFRL=238,0;MMQ=60,60;MPOS=7;NALOD=1.19;NLOD=4.21;POPAF=6.00;TLOD=15.96 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:19,0:0.061:19:9,0:5,0:14,0:12,7,0,0 0/1:0,4:0.833:4:0,0:0,4:0,4:0,0,4,0
chr12 98626070 . TATC T . clustered_events;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=39,11|14,0;DP=66;ECNT=3;GERMQ=53;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=73;NALOD=0.124;NLOD=3.20;POPAF=6.00;TLOD=46.67 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:18,1:0.092:19:9,1:5,0:18,1:13,5,1,0 0/1:32,13:0.326:45:2,0:26,13:28,13:26,6,13,0
chr12 98626173 . CA AT . clustered_events;normal_artifact;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=90,69|19,0;DP=206;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=15;NALOD=0.878;NLOD=14.78;POPAF=6.00;TLOD=51.05 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:60,3:0.032:63:26,1:29,0:59,3:13,47,3,0 0/1:99,16:0.151:115:0,0:71,16:94,16:77,22,16,0
chr12 98626192 . AT A . clustered_events;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=124,100|14,3;DP=246;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=65;NALOD=1.82;NLOD=22.38;POPAF=6.00;TLOD=35.89 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:88,3:0.017:91:36,0:43,0:84,3:19,69,0,3 0/1:136,14:0.109:150:0,0:105,14:122,14:105,31,14,0
chr12 98626486 . T G . strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=135,224|0,19;DP=378;ECNT=1;GERMQ=93;MBQ=35,37;MFRL=144,0;MMQ=60,60;MPOS=72;NALOD=2.24;NLOD=51.76;POPAF=6.00;TLOD=46.10 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:229,0:5.734e-03:229:73,0:92,0:172,0:95,134,0,0 0/1:130,19:0.141:149:74,17:37,0:115,19:40,90,0,19
chr12 98634388 . A AT . PASS AS_FilterStatus=SITE;AS_SB_TABLE=227,143|13,6;DP=401;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=59;NALOD=1.69;NLOD=13.09;POPAF=6.00;RPA=5,6;RU=T;STR;STRQ=93;TLOD=33.79 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:53,0:0.020:53:16,0:19,0:45,0:26,27,0,0 0/1:317,19:0.058:336:43,2:206,13:257,15:201,116,13,6
chr12 98648352 . GA G . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=243,266|1,12;DP=606;ECNT=6;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=24;NALOD=1.69;NLOD=16.51;POPAF=6.00;TLOD=23.50 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:61,1:0.020:62:31,0:27,0:59,1:53,8,1,0 0/1:448,12:0.040:460:103,8:186,0:311,12:190,258,0,12
chr12 98648361 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=275,308|12,11;DP=619;ECNT=6;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=37;NALOD=1.77;NLOD=16.29;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=61.37 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:57,0:0.017:57:28,0:26,0:55,0:49,8,0,0 0/1:526,23:0.034:549:139,0:220,12:369,12:226,300,12,11
chr12 98648406 . T G . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=238,342|11,11;DP=605;ECNT=6;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=41;NALOD=1.64;NLOD=11.94;POPAF=6.00;TLOD=61.74 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:44,0:0.022:44:19,0:18,0:40,0:29,15,0,0 0/1:536,22:0.031:558:147,0:202,10:372,11:209,327,11,11
chr12 98648436 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=191,368|16,14;DP=595;ECNT=6;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=43;NALOD=1.68;NLOD=13.57;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=81.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:48,0:0.020:48:17,0:17,0:46,0:12,36,0,0 0/1:511,30:0.044:541:141,0:175,16:371,17:179,332,16,14
chr12 98648455 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=163,383|10,14;DP=577;ECNT=6;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=10;NALOD=1.63;NLOD=12.05;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=59.39 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:43,0:0.023:43:15,0:15,0:41,0:7,36,0,0 0/1:503,24:0.040:527:142,5:161,10:378,15:156,347,10,14
chr12 98648457 . G A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=164,391|9,6;DP=577;ECNT=6;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=21;NALOD=1.63;NLOD=11.82;POPAF=6.00;TLOD=35.01 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:42,0:0.023:42:13,0:13,0:40,0:7,35,0,0 0/1:513,15:0.025:528:147,0:153,9:384,9:157,356,9,6
chr12 98649541 . CA C . clustered_events;haplotype AS_FilterStatus=SITE;AS_SB_TABLE=530,133|14,1;DP=690;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=46;NALOD=2.17;NLOD=43.88;POPAF=6.00;RPA=2,1;RU=A;STR;STRQ=93;TLOD=17.02 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:159,1:6.729e-03:160:68,0:70,0:148,1:0|1:98649541_CA_C:98649541:119,40,0,1 0|1:504,14:0.021:518:39,0:368,14:453,14:0|1:98649541_CA_C:98649541:411,93,14,0
chr12 98649544 . G T . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=530,133|14,1;DP=693;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=44;NALOD=2.17;NLOD=43.87;POPAF=6.00;TLOD=17.01 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:159,1:6.837e-03:160:62,0:70,0:148,1:0|1:98649541_CA_C:98649541:119,40,0,1 0|1:504,14:0.021:518:39,0:403,9:453,14:0|1:98649541_CA_C:98649541:411,93,14,0
chr12 98649583 . AATTG A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=609,283|2,8;DP=923;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=60;NALOD=2.04;NLOD=30.67;POPAF=6.00;TLOD=24.26 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:105,0:9.099e-03:105:47,0:42,0:102,0:62,43,0,0 0/1:787,10:0.014:797:54,6:524,2:649,8:547,240,2,8
chr12 98649586 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=594,270|12,12;DP=906;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=41;NALOD=1.71;NLOD=29.45;POPAF=6.00;TLOD=55.14 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:101,0:9.786e-03:101:42,0:43,0:99,0:59,42,0,0 0/1:763,24:0.020:787:53,0:530,12:637,12:535,228,12,12
chr12 98649587 . G A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=579,262|27,20;DP=906;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=59;NALOD=1.71;NLOD=29.30;POPAF=6.00;TLOD=52.61 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:101,0:9.807e-03:101:41,0:40,0:99,0:59,42,0,0 0/1:740,47:0.038:787:55,1:514,15:618,31:520,220,27,20
chr12 98649591 . G A . clustered_events;normal_artifact;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=658,292|3,3;DP=996;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=26;NALOD=0.859;NLOD=23.37;POPAF=6.00;TLOD=8.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:93,2:0.024:95:39,0:37,1:91,2:51,42,1,1 0/1:857,4:4.135e-03:861:65,0:579,2:720,2:607,250,2,2
chr12 98649592 . G T . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=659,305|6,0;DP=996;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=26;NALOD=1.98;NLOD=27.60;POPAF=6.00;TLOD=5.33 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:95,0:0.010:95:40,0:36,0:93,0:53,42,0,0 0/1:869,6:9.471e-03:875:67,0:590,6:719,6:606,263,6,0
chr12 98649641 . TGTATTA T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=669,639|6,0;DP=1317;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=54;NALOD=1.89;NLOD=22.53;POPAF=6.00;TLOD=9.35 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:79,0:0.013:79:31,0:29,0:75,0:15,64,0,0 0/1:1229,6:8.071e-03:1235:93,0:630,6:856,6:654,575,6,0
chr12 98649653 . AG A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=644,664|22,6;DP=1375;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=64;NALOD=1.81;NLOD=18.73;POPAF=6.00;TLOD=57.56 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:69,1:0.015:70:28,1:29,0:65,1:11,58,0,1 0/1:1239,27:0.031:1266:130,1:631,26:860,27:633,606,22,5
chr12 98649674 . CC TC,TT . clustered_events;multiallelic AS_FilterStatus=SITE|strand_bias;AS_SB_TABLE=605,808|5,6|4,3;DP=1451;ECNT=16;GERMQ=93;MBQ=37,37,37;MFRL=0,0,0;MMQ=60,60,60;MPOS=25,65;NALOD=1.44,1.49;NLOD=16.49,17.65;POPAF=6.00,6.00;TLOD=29.41,15.91 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:60,1,0:0.018,0.016:61:22,1,0:24,0,0:58,1,0:7,53,0,1 0/1/2:1353,10,7:6.031e-03,5.011e-03:1370:165,0,0:575,5,4:982,5,4:598,755,9,8
chr12 98649675 . CT CTT,TT,C,CTTT . clustered_events;multiallelic AS_FilterStatus=SITE|strand_bias|SITE|strand_bias;AS_SB_TABLE=483,726|65,60|4,20|5,6|2,2;DP=1451;ECNT=16;GERMQ=93;MBQ=37,37,37,37,37;MFRL=0,0,0,0,0;MMQ=60,60,60,60,60;MPOS=43,35,24,47;NALOD=1.10,0.257,1.06,1.10;NLOD=16.20,14.70,16.43,16.79;POPAF=6.00,6.00,6.00,6.00;TLOD=307.61,28.29,29.80,6.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:58,0,1,1,0:0.016,0.030,0.017,0.016:60:21,0,1,1,0:24,0,0,0,0:56,0,1,1,0:6,52,0,2 0/1/2/3/4:1151,125,23,10,4:0.083,0.017,6.042e-03,3.094e-03:1313:152,10,1,0,0:483,63,3,5,1:853,79,20,5,2:477,674,76,86
chr12 98649679 . TA T . clustered_events;haplotype AS_FilterStatus=SITE;AS_SB_TABLE=556,812|3,4;DP=1395;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=30;NALOD=1.76;NLOD=16.85;POPAF=6.00;TLOD=17.95 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:58,0:0.017:58:23,0:24,0:56,0:0|1:98649679_TA_T:98649679:6,52,0,0 0|1:1310,7:5.169e-03:1317:167,0:535,3:959,4:0|1:98649679_TA_T:98649679:550,760,3,4
chr12 98649680 . A T . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=553,809|3,3;DP=1382;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=48;NALOD=1.47;NLOD=16.78;POPAF=6.00;TLOD=13.43 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:58,0:0.017:58:23,0:22,0:56,0:6,52,0,0 0/1:1304,6:4.156e-03:1310:167,0:526,3:956,3:547,757,3,3
chr12 98649681 . G T . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=556,812|3,4;DP=1376;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=31;NALOD=1.76;NLOD=16.85;POPAF=6.00;TLOD=17.95 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:58,0:0.017:58:22,0:24,0:56,0:0|1:98649679_TA_T:98649679:6,52,0,0 0|1:1310,7:5.169e-03:1317:167,0:534,3:959,4:0|1:98649679_TA_T:98649679:550,760,3,4
chr12 98649683 . AG A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=521,766|6,7;DP=1363;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=23;NALOD=1.76;NLOD=16.63;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=28.71 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:58,0:0.017:58:23,0:23,0:56,0:6,52,0,0 0/1:1229,13:8.689e-03:1242:154,0:493,6:908,7:515,714,6,7
chr12 98649700 . C T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=112,335|3,3;DP=453;ECNT=16;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=47;NALOD=1.72;NLOD=15.61;POPAF=6.00;TLOD=14.71 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:54,0:0.019:54:21,0:21,0:52,0:6,48,0,0 0/1:393,6:0.013:399:61,0:104,3:305,3:106,287,3,3
chr12 98662757 . G C . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=31,114|0,15;DP=163;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=74;NALOD=1.65;NLOD=12.52;POPAF=6.00;TLOD=42.54 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:48,0:0.022:48:13,0:18,0:42,0:0|1:98662757_G_C:98662757:28,20,0,0 0|1:97,15:0.143:112:87,15:3,0:95,15:0|1:98662757_G_C:98662757:3,94,0,15
chr12 98662762 . CAG C . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=31,117|0,11;DP=163;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=69;NALOD=1.63;NLOD=12.01;POPAF=6.00;TLOD=32.73 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:45,0:0.023:45:12,0:18,0:40,0:1|0:98662757_G_C:98662757:25,20,0,0 1|0:103,11:0.105:114:92,11:6,0:101,11:1|0:98662757_G_C:98662757:6,97,0,11
chr12 98662784 . TAG T . clustered_events;haplotype AS_FilterStatus=SITE;AS_SB_TABLE=24,98|0,11;DP=134;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=49;NALOD=1.54;NLOD=10.23;POPAF=6.00;TLOD=33.86 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:40,0:0.028:40:8,0:15,0:34,0:1|0:98662757_G_C:98662757:18,22,0,0 1|0:82,11:0.129:93:68,11:6,0:80,11:1|0:98662757_G_C:98662757:6,76,0,11
chr12 98665538 . A AT . slippage;weak_evidence AS_FilterStatus=weak_evidence;AS_SB_TABLE=38,57|1,2;DP=100;ECNT=1;GERMQ=93;MBQ=20,37;MFRL=176,0;MMQ=60,60;MPOS=37;NALOD=1.82;NLOD=18.41;POPAF=6.00;RPA=10,11;RU=T;STR;STRQ=1;TLOD=3.51 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:81,1:0.015:82:25,0:43,1:69,1:28,53,0,1 0/1:14,2:0.154:16:4,1:6,0:10,1:10,4,1,1
chr12 98665698 . CAT C . clustered_events;haplotype AS_FilterStatus=SITE;AS_SB_TABLE=98,23|10,0;DP=134;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=67;NALOD=1.80;NLOD=17.74;POPAF=6.00;TLOD=31.84 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:61,0:0.016:61:24,0:32,0:59,0:0|1:98665698_CAT_C:98665698:46,15,0,0 0|1:60,10:0.162:70:0,0:50,9:56,10:0|1:98665698_CAT_C:98665698:52,8,10,0
chr12 98665701 . G C . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=98,29|10,0;DP=137;ECNT=4;GERMQ=93;MBQ=36,37;MFRL=0,0;MMQ=60,60;MPOS=66;NALOD=1.79;NLOD=17.74;POPAF=6.00;TLOD=31.84 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:61,0:0.016:61:24,0:29,0:59,0:0|1:98665698_CAT_C:98665698:46,15,0,0 0|1:66,10:0.162:76:1,0:50,9:56,10:0|1:98665698_CAT_C:98665698:52,14,10,0
chr12 98665709 . G T . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=100,33|10,0;DP=148;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=58;NALOD=1.74;NLOD=15.94;POPAF=6.00;TLOD=31.05 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:54,0:0.018:54:22,0:25,0:53,0:0|1:98665698_CAT_C:98665698:40,14,0,0 0|1:79,10:0.139:89:1,0:57,9:67,10:0|1:98665698_CAT_C:98665698:60,19,10,0
chr12 98665796 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=29,66|6,7;DP=109;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=33;NALOD=1.46;NLOD=8.25;POPAF=6.00;RPA=3,2;RU=G;STR;STRQ=93;TLOD=36.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:30,0:0.034:30:9,0:10,0:28,0:5,25,0,0 0/1:65,13:0.130:78:14,1:24,5:52,7:24,41,6,7
chr12 98666214 . G A . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=132,43|15,0;DP=190;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=67;NALOD=1.80;NLOD=18.56;POPAF=6.00;TLOD=40.72 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:69,0:0.016:69:31,0:30,0:62,0:62,7,0,0 0/1:106,15:0.131:121:34,0:68,15:105,15:70,36,15,0
chr12 98666348 . C A . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=227,131|1,19;DP=380;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=4;NALOD=1.83;NLOD=19.87;POPAF=6.00;TLOD=45.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:71,0:0.015:71:21,0:22,0:66,0:0|1:98666348_C_A:98666348:6,65,0,0 0|1:287,20:0.071:307:33,18:214,0:265,20:0|1:98666348_C_A:98666348:221,66,1,19
chr12 98666352 . C A . base_qual;clustered_events;haplotype;strand_bias AS_FilterStatus=base_qual,strand_bias;AS_SB_TABLE=227,131|1,19;DP=378;ECNT=3;GERMQ=93;MBQ=37,11;MFRL=0,0;MMQ=60,60;MPOS=5;NALOD=1.83;NLOD=19.87;POPAF=6.00;TLOD=45.49 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:71,0:0.015:71:20,0:23,0:66,0:0|1:98666348_C_A:98666348:6,65,0,0 0|1:287,20:0.071:307:33,0:213,0:265,20:0|1:98666348_C_A:98666348:221,66,1,19
chr12 98670994 . T C . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=138,72|0,11;DP=223;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=29;NALOD=1.75;NLOD=16.49;POPAF=6.00;TLOD=27.25 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:59,0:0.017:59:27,0:28,0:55,0:50,9,0,0 0/1:151,11:0.074:162:60,11:87,0:149,11:88,63,0,11
chr12 98671043 . TG T . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=123,166|24,0;DP=315;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=74;NALOD=1.69;NLOD=14.34;POPAF=6.00;TLOD=61.51 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:58,0:0.020:58:20,0:24,0:48,0:34,24,0,0 0/1:231,24:0.100:255:131,0:85,23:223,24:89,142,24,0
chr12 98671060 . GAA G . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=149,154|0,11;DP=321;ECNT=3;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=55;NALOD=1.66;NLOD=13.23;POPAF=6.00;TLOD=28.33 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:54,0:0.022:54:18,0:20,0:44,0:29,25,0,0 0/1:249,11:0.047:260:119,11:113,0:243,11:120,129,0,11
chr12 98671506 . G GT . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=89,2|15,0;DP=106;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=58;NALOD=1.25;NLOD=5.96;POPAF=6.00;RPA=3,4;RU=T;STR;STRQ=93;TLOD=29.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:23,1:0.052:24:12,0:11,1:23,1:21,2,1,0 0/1:68,14:0.178:82:0,0:68,14:68,14:68,0,14,0
chr12 98671551 . AG A . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=234,91|14,0;DP=367;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=45;NALOD=1.37;NLOD=6.28;POPAF=6.00;TLOD=29.84 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:21,0:0.042:21:9,0:10,0:21,0:15,6,0,0 0/1:304,14:0.050:318:62,0:209,14:286,14:219,85,14,0
chr12 98671660 . G T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=574,553|8,23;DP=1175;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=9;NALOD=1.92;NLOD=24.25;POPAF=6.00;TLOD=66.87 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:82,0:0.012:82:43,0:32,0:81,0:22,60,0,0 0/1:1045,31:0.029:1076:187,2:536,7:812,25:552,493,8,23
chr12 98671703 . C T,CT . clustered_events;multiallelic AS_FilterStatus=strand_bias|SITE;AS_SB_TABLE=502,556|46,3|3,4;DP=1145;ECNT=4;GERMQ=93;MBQ=37,37,37;MFRL=0,0,0;MMQ=60,60,60;MPOS=41,47;NALOD=1.70,1.70;NLOD=29.34,28.06;POPAF=6.00,6.00;TLOD=123.73,10.72 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:100,0,0:9.800e-03,0.010:100:49,0,0:44,0,0:97,0,0:12,88,0,0 0/1/2:958,49,7:0.057,6.044e-03:1014:134,0,1:472,46,3:764,46,4:490,468,49,7
chr12 98677568 . GA G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=95,92|6,8;DP=212;ECNT=1;GERMQ=93;MBQ=25,37;MFRL=157,0;MMQ=60,60;MPOS=9;NALOD=0.610;NLOD=27.07;POPAF=6.00;TLOD=43.19 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:125,1:0.019:126:43,0:38,1:101,1:72,53,0,1 0/1:62,13:0.166:75:13,1:23,6:39,7:23,39,6,7
chr12 98680356 . CAG C . clustered_events;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=211,345|9,17;DP=616;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=68;NALOD=2.01;NLOD=33.79;POPAF=6.00;TLOD=66.69 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:133,2:0.011:135:51,0:61,0:120,2:82,51,0,2 0/1:423,24:0.060:447:260,14:127,8:389,24:129,294,9,15
chr12 98680386 . TG T . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=228,399|0,9;DP=642;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=65;NALOD=1.98;NLOD=27.50;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=12.15 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:106,0:0.010:106:41,0:43,0:93,0:51,55,0,0 0/1:521,9:0.021:530:281,9:171,0:461,9:177,344,0,9
chr12 98680389 . AT A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=218,405|6,12;DP=659;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=63;NALOD=1.65;NLOD=25.42;POPAF=6.00;TLOD=28.55 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:99,0:0.011:99:38,0:39,0:86,0:46,53,0,0 0/1:524,18:0.035:542:278,9:169,5:458,18:172,352,6,12
chr12 98680390 . T A . clustered_events;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=212,405|12,4;DP=656;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=29;NALOD=1.57;NLOD=24.25;POPAF=6.00;TLOD=7.45 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:99,1:0.014:100:38,0:38,0:86,1:46,53,0,1 0/1:518,15:0.016:533:279,0:162,6:452,15:166,352,12,3
chr12 98686825 . AC A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=323,125|16,1;DP=483;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=56;NALOD=1.89;NLOD=22.95;POPAF=6.00;RPA=2,1;RU=C;STR;STRQ=93;TLOD=30.13 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:101,1:0.013:102:39,0:37,0:80,1:51,50,0,1 0/1:347,16:0.048:363:57,0:261,16:336,16:272,75,16,0
chr12 98699416 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=158,155|5,6;DP=334;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=15;NALOD=1.83;NLOD=19.72;POPAF=6.00;TLOD=31.20 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:68,0:0.015:68:32,0:34,0:66,0:57,11,0,0 0/1:245,11:0.034:256:81,1:96,5:200,6:101,144,5,6
chr12 98699535 . CA C . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=538,630|8,10;DP=1231;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=34;NALOD=1.90;NLOD=27.64;POPAF=6.00;RPA=2,1;RU=A;STR;STRQ=93;TLOD=25.77 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:102,1:0.013:103:45,1:42,0:99,1:18,84,0,1 0/1:1066,17:0.021:1083:255,9:514,7:817,17:520,546,8,9
chr12 98699549 . G A . clustered_events;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=537,534|20,27;DP=1211;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=4;NALOD=-4.709e-02;NLOD=25.56;POPAF=6.00;TLOD=119.57 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:100,2:0.020:102:44,1:39,0:99,1:12,88,1,1 0/1:971,45:0.045:1016:239,7:513,19:782,36:525,446,19,26
chr12 98699553 . C CA . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=463,421|31,24;DP=1121;ECNT=4;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=51;NALOD=1.99;NLOD=27.17;POPAF=6.00;RPA=6,7;RU=A;STR;STRQ=93;TLOD=88.13 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:97,0:0.010:97:44,0:34,0:96,0:9,88,0,0 0/1:787,55:0.071:842:187,5:445,37:655,50:454,333,31,24
chr12 98703361 . A G . strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=157,99|13,0;DP=272;ECNT=1;GERMQ=93;MBQ=20,37;MFRL=167,0;MMQ=60,60;MPOS=3;NALOD=2.12;NLOD=38.51;POPAF=6.00;TLOD=35.09 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:192,0:7.624e-03:192:66,0:61,0:128,0:109,83,0,0 0/1:64,13:0.173:77:16,0:47,12:64,13:48,16,13,0
chr12 98708684 . G T . strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=160,195|19,0;DP=377;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=42;NALOD=1.95;NLOD=26.42;POPAF=6.00;TLOD=46.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:141,0:0.011:141:32,0:51,0:88,0:73,68,0,0 0/1:214,19:0.096:233:91,0:87,18:182,19:87,127,19,0
chr12 98723180 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=77,17|9,0;DP=112;ECNT=2;GERMQ=93;MBQ=36,37;MFRL=138,0;MMQ=60,60;MPOS=21;NALOD=1.73;NLOD=15.82;POPAF=6.00;TLOD=26.59 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:54,0:0.018:54:24,0:27,0:53,0:48,6,0,0 0/1:40,9:0.250:49:0,0:29,9:29,9:29,11,9,0
chr12 98723279 . ACTG A . strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=118,77|0,11;DP=208;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=42;NALOD=1.61;NLOD=11.41;POPAF=6.00;TLOD=30.85 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:42,0:0.024:42:19,0:16,0:38,0:18,24,0,0 0/1:153,11:0.074:164:24,0:100,0:150,11:100,53,0,11
chr12 98725418 . TG T . normal_artifact;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=191,291|20,1;DP=527;ECNT=1;GERMQ=93;MBQ=35,37;MFRL=0,0;MMQ=60,60;MPOS=28;NALOD=1.78;NLOD=49.63;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=38.60 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:230,3:0.011:233:94,2:75,1:180,3:93,137,3,0 0/1:252,18:0.080:270:105,1:92,17:216,18:98,154,17,1
chr12 98727163 . G GT . strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=102,109|16,0;DP=239;ECNT=1;GERMQ=93;MBQ=20,37;MFRL=173,0;MMQ=60,60;MPOS=40;NALOD=2.10;NLOD=36.92;POPAF=6.00;RPA=3,4;RU=T;STR;STRQ=93;TLOD=29.79 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:162,3:8.069e-03:165:64,0:60,1:130,1:60,102,3,0 0/1:49,13:0.245:62:0,0:41,13:42,13:42,7,13,0
chr12 98732492 . G T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=261,233|13,13;DP=529;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=57;NALOD=2.28;NLOD=55.57;POPAF=6.00;TLOD=81.37 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:207,0:5.232e-03:207:84,0:95,0:186,0:168,39,0,0 0/1:287,26:0.056:313:144,0:89,13:237,13:93,194,13,13
chr12 98732613 . G A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=2,183|0,15;DP=200;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=23;NALOD=1.49;NLOD=9.03;POPAF=6.00;TLOD=37.59 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:31,0:0.031:31:2,0:2,0:30,0:2,29,0,0 0/1:154,15:0.094:169:108,0:0,0:154,15:0,154,0,15
chr12 98735024 . G A . clustered_events;haplotype;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=138,0|11,0;DP=149;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=75;NALOD=-1.692e+00;NLOD=4.79;POPAF=6.00;TLOD=25.66 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:34,2:0.078:36:21,0:13,0:34,2:0|1:98735024_G_A:98735024:34,0,2,0 0|1:104,9:0.087:113:0,0:104,9:104,9:0|1:98735024_G_A:98735024:104,0,9,0
chr12 98735029 . C T . clustered_events;haplotype;normal_artifact AS_FilterStatus=SITE;AS_SB_TABLE=141,0|12,0;DP=153;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=70;NALOD=-1.789e+00;NLOD=4.32;POPAF=6.00;TLOD=25.54 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:34,3:0.083:37:21,2:13,1:34,3:0|1:98735024_G_A:98735024:34,0,3,0 0|1:107,9:0.085:116:0,0:101,9:107,9:0|1:98735024_G_A:98735024:107,0,9,0
chr12 98735070 . A G . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=172,167|2,2;DP=344;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=27;NALOD=1.55;NLOD=10.24;POPAF=6.00;TLOD=11.40 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:35,0:0.027:35:21,0:13,0:34,0:33,2,0,0 0/1:304,4:0.015:308:11,0:136,2:198,2:139,165,2,2
chr12 98735085 . AG A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=172,166|9,10;DP=363;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=46;NALOD=1.57;NLOD=10.74;POPAF=6.00;TLOD=54.17 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:37,0:0.026:37:21,0:14,0:36,0:34,3,0,0 0/1:301,19:0.052:320:11,1:131,9:201,10:138,163,9,10
chr12 98735086 . GAA G,AAA . clustered_events;multiallelic AS_FilterStatus=strand_bias|SITE;AS_SB_TABLE=178,159|0,15|4,5;DP=363;ECNT=9;GERMQ=93;MBQ=37,37,37;MFRL=0,0,0;MMQ=60,60,60;MPOS=47,45;NALOD=1.12,1.12;NLOD=10.79,11.13;POPAF=6.00,6.00;TLOD=42.05,12.03 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:37,0,0:0.025,0.025:37:21,0,0:15,0,0:36,0,0:34,3,0,0 0/1/2:300,15,9:0.075,0.028:324:11,0,1:136,0,4:194,15,5:144,156,4,20
chr12 98735088 . A G . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=180,161|3,3;DP=362;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=38;NALOD=1.28;NLOD=10.75;POPAF=6.00;TLOD=12.52 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:37,0:0.026:37:21,0:14,0:36,0:34,3,0,0 0/1:304,6:0.020:310:13,0:138,3:196,3:146,158,3,3
chr12 98735147 . T C . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=176,194|13,13;DP=398;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=45;NALOD=1.48;NLOD=8.39;POPAF=6.00;TLOD=82.72 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:28,0:0.032:28:15,0:12,0:28,0:16,12,0,0 0/1:342,26:0.047:368:24,0:160,13:281,13:160,182,13,13
chr12 98735205 . G T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=102,63|7,7;DP=183;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=34;NALOD=1.40;NLOD=7.16;POPAF=6.00;TLOD=42.06 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:24,0:0.038:24:11,0:10,0:24,0:8,16,0,0 0/1:141,14:0.060:155:21,0:93,6:124,7:94,47,7,7
chr12 98735265 . TG T . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=17,148|6,7;DP=204;ECNT=9;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=70;NALOD=1.49;NLOD=8.57;POPAF=6.00;RPA=2,1;RU=G;STR;STRQ=93;TLOD=35.65 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:30,0:0.031:30:11,0:16,0:29,0:1,29,0,0 0/1:135,13:0.062:148:24,1:16,6:119,7:16,119,6,7
chr12 98735323 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=5,131|0,9;DP=145;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=0,0;MMQ=60,60;MPOS=43;NALOD=1.23;NLOD=4.72;POPAF=6.00;TLOD=22.29 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:16,0:0.056:16:6,0:8,0:16,0:2,14,0,0 0/1:120,9:0.078:129:111,9:3,0:117,9:3,117,0,9
chr12 98735410 . T A . PASS AS_FilterStatus=SITE;AS_SB_TABLE=12,6|6,0;DP=25;ECNT=2;GERMQ=44;MBQ=37,37;MFRL=267,0;MMQ=60,60;MPOS=49;NALOD=1.09;NLOD=3.31;POPAF=6.00;TLOD=20.68 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:11,0:0.075:11:6,0:5,0:11,0:5,6,0,0 0/1:7,6:0.467:13:0,0:7,6:7,6:7,0,6,0
chr12 98735568 . TTC T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=110,143|8,7;DP=276;ECNT=2;GERMQ=93;MBQ=20,37;MFRL=169,0;MMQ=60,60;MPOS=51;NALOD=2.24;NLOD=50.94;POPAF=6.00;TLOD=54.14 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:212,0:5.728e-03:212:83,0:71,0:170,0:0|1:98735568_TTC_T:98735568:87,125,0,0 0|1:41,15:0.196:56:0,0:23,8:36,8:0|1:98735568_TTC_T:98735568:23,18,8,7
chr12 98735570 . C T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=108,139|8,12;DP=274;ECNT=2;GERMQ=93;MBQ=20,37;MFRL=169,0;MMQ=60,60;MPOS=49;NALOD=1.94;NLOD=50.64;POPAF=6.00;TLOD=10.24 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:210,0:5.762e-03:210:83,0:72,0:169,0:1|0:98735568_TTC_T:98735568:85,125,0,0 1|0:37,20:0.191:57:0,0:23,0:32,12:1|0:98735568_TTC_T:98735568:23,14,8,12
chr12 98794907 . G A . clustered_events AS_FilterStatus=SITE;AS_SB_TABLE=96,80|11,2;DP=192;ECNT=3;GERMQ=93;MBQ=20,37;MFRL=192,0;MMQ=60,60;MPOS=39;NALOD=2.09;NLOD=36.63;POPAF=6.00;TLOD=48.80 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:176,0:8.020e-03:176:48,0:69,0:122,0:96,80,0,0 0/1:0,13:0.923:13:0,0:0,10:0,11:0,0,11,2
chr12 98794927 . C T . clustered_events;haplotype;strand_bias AS_FilterStatus=strand_bias;AS_SB_TABLE=68,86|9,0;DP=164;ECNT=3;GERMQ=93;MBQ=20,37;MFRL=195,0;MMQ=60,60;MPOS=19;NALOD=2.04;NLOD=32.19;POPAF=6.00;TLOD=39.50 GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB 0|0:154,0:9.140e-03:154:35,0:55,0:107,0:0|1:98794927_C_T:98794927:68,86,0,0 0|1:0,9:0.909:9:0,0:0,9:0,9:0|1:98794927_C_T:98794927:0,0,9,0 -
The issue you are facing is a known issue that an uncaught edge case which is being pursued by our team currently. In the mean time you may try using the GATK master branch build or docker nightlies with resource bundle version 1.8 to see if you problem still persists. If it is then we can start a github issue to track the problem further.
I hope this helps.
Reason for edit: Wrong wording. (replace: known edge case > known issue that an uncaught edge case)
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Hi,
What exactly is a "known edge case"?
I've used 1.7 for quite a while without problems. The link given on the resource-bundle site does not have 1.8. The link seems to date to 2016? I got 1.7 from google cloud site but not this one.
Thanks,
https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle
https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/
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I meant although Funcotator is thoroughly tested this issue of string length error is a known one that happens only when the code reaches some uncaught edge cases which could be due to changes in the resources that we produce our resource files such as Gencode definition files. Our team is improving the code to eliminate these issues therefore we are generating new versions of the resources and new Funcotator code.
The next target resource files are found in the google bucket in the repository below
https://console.cloud.google.com/storage/browser/broad-public-datasets/funcotator
The version 1.8 is targeted for the next release of GATK 4.5.0.0 which will be available soon. For the time being updates to the Funcotator code and compatibility with resource version 1.8 is already available in the GATK master branch and docker nightly builds. If you wish to try it we would be happy to hear if you hit the same issue with the latest code and so we can start a github issue to track the problem.
Regards.
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