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FilterMutectCalls (gatk 4.0.12.0) fails due to the probability value of NaN #5553

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byoo opened this issue Dec 28, 2018 · 15 comments · Fixed by #5563
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FilterMutectCalls (gatk 4.0.12.0) fails due to the probability value of NaN #5553

byoo opened this issue Dec 28, 2018 · 15 comments · Fixed by #5563
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@davidbenjamin
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bug Mutect PRIORITY_HIGH

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@byoo
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byoo commented Dec 28, 2018 •
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Hello,

I'd like to report a FilterMutectCalls error. It was run using mutect2.wdl with gatk 4.0.12.0.
FilterMutectCalls of gatk 4.0.10.1 succeeded using same input.
Please let me know if there is something else I can provide. Thank you.

java.lang.IllegalArgumentException: errorRateLog10 must be good probability but got NaN
        at org.broadinstitute.hellbender.utils.QualityUtils.phredScaleLog10ErrorRate(QualityUtils.java:321)
        at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.lambda$applyGermlineVariantFilter$10(Mutect2FilteringEngine.java:207)
        at java.util.stream.DoublePipeline$3$1.accept(DoublePipeline.java:231)
        at java.util.Spliterators$DoubleArraySpliterator.forEachRemaining(Spliterators.java:1198)
        at java.util.Spliterator$OfDouble.forEachRemaining(Spliterator.java:822)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
        at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
        at java.util.stream.IntPipeline.toArray(IntPipeline.java:502)
        at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.applyGermlineVariantFilter(Mutect2FilteringEngine.java:207)
        at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.calculateFilters(Mutect2FilteringEngine.java:436)
        at org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls.firstPassApply(FilterMutectCalls.java:120)
        at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.lambda$traverseVariants$0(TwoPassVariantWalker.java:76)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
        at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
        at java.util.Iterator.forEachRemaining(Iterator.java:116)
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
        at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
        at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverseVariants(TwoPassVariantWalker.java:74)
        at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverse(TwoPassVariantWalker.java:27)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        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)
Using GATK jar /gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/0c2281d2-9d90-4ee3-88bb-f0bb015cdb7c/call-Filter/attempt-4/inputs/392945202/gatk-package-4.0.12.0-local.jar defined in environment variable GATK_LOCAL_JAR
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6500m -jar /gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/0c2281d2-9d90-4ee3-88bb-f0bb015cdb7c/call-Filter/attempt-4/inputs/392945202/gatk-package-4.0.12.0-local.jar FilterMutectCalls -V /gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/0c2281d2-9d90-4ee3-88bb-f0bb015cdb7c/call-Filter/attempt-4/inputs/-356078842/Ameloblastoma_FFPE_P5-unfiltered.vcf.gz -O Ameloblastoma_FFPE_P5-filtered.vcf.gz --contamination-table /gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/0c2281d2-9d90-4ee3-88bb-f0bb015cdb7c/call-Filter/attempt-4/inputs/51739658/contamination.table --tumor-segmentation /gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/0c2281d2-9d90-4ee3-88bb-f0bb015cdb7c/call-Filter/attempt-4/inputs/51739658/segments.table --max-events-in-region 6
@davidbenjamin davidbenjamin self-assigned this Dec 31, 2018
@davidbenjamin
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@byoo Could you take the unfiltered vcf: /gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/0c2281d2-9d90-4ee3-88bb-f0bb015cdb7c/call-Filter/attempt-4/inputs/-356078842/Ameloblastoma_FFPE_P5-unfiltered.vcf.gz, and restrict it to a small interval (at big as one chromosome and small as just the problematic site) surrounding the variant that causes the error? If the stderr isn't enough to identify the site approximately, you could run gatk FilterMutectCalls -V unfiltered.vcf -O tmp.vcf locally without any of the optional inputs and I believe tmp.vcf would be produced with every site up to but not including the problematic one.

@MikeWLloyd
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I've hit the same issue. I can't say for certain the files I'm using run cleanly, because I had been getting the error associated with 'AF=.' #5442.

2019-01-04T14:02:27.214488889Z [January 4, 2019 2:02:27 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls done. Elapsed time: 0.05 minutes.
2019-01-04T14:02:27.214810448Z Runtime.totalMemory()=407896064
2019-01-04T14:02:27.215613324Z java.lang.IllegalArgumentException: errorRateLog10 must be good probability but got NaN
2019-01-04T14:02:27.216082142Z 	at org.broadinstitute.hellbender.utils.QualityUtils.phredScaleLog10ErrorRate(QualityUtils.java:321)
2019-01-04T14:02:27.216288993Z 	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.lambda$applyGermlineVariantFilter$10(Mutect2FilteringEngine.java:207)
2019-01-04T14:02:27.216482786Z 	at java.util.stream.DoublePipeline$3$1.accept(DoublePipeline.java:231)
2019-01-04T14:02:27.216675396Z 	at java.util.Spliterators$DoubleArraySpliterator.forEachRemaining(Spliterators.java:1198)
2019-01-04T14:02:27.216858104Z 	at java.util.Spliterator$OfDouble.forEachRemaining(Spliterator.java:822)
2019-01-04T14:02:27.217027544Z 	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
2019-01-04T14:02:27.234512924Z 	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
2019-01-04T14:02:27.234886181Z 	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
2019-01-04T14:02:27.235138770Z 	at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
2019-01-04T14:02:27.235509109Z 	at java.util.stream.IntPipeline.toArray(IntPipeline.java:502)
2019-01-04T14:02:27.235661751Z 	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.applyGermlineVariantFilter(Mutect2FilteringEngine.java:207)
2019-01-04T14:02:27.235931663Z 	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.calculateFilters(Mutect2FilteringEngine.java:436)
2019-01-04T14:02:27.236174900Z 	at org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls.firstPassApply(FilterMutectCalls.java:120)
2019-01-04T14:02:27.236322702Z 	at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.lambda$traverseVariants$0(TwoPassVariantWalker.java:76)
2019-01-04T14:02:27.237171464Z 	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
2019-01-04T14:02:27.237239651Z 	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
2019-01-04T14:02:27.237250455Z 	at java.util.Iterator.forEachRemaining(Iterator.java:116)
2019-01-04T14:02:27.237256726Z 	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
2019-01-04T14:02:27.237294098Z 	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
2019-01-04T14:02:27.237302853Z 	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
2019-01-04T14:02:27.237308231Z 	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
2019-01-04T14:02:27.237342232Z 	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
2019-01-04T14:02:27.237377382Z 	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
2019-01-04T14:02:27.237384696Z 	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
2019-01-04T14:02:27.237442143Z 	at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverseVariants(TwoPassVariantWalker.java:74)
2019-01-04T14:02:27.237452377Z 	at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverse(TwoPassVariantWalker.java:27)
2019-01-04T14:02:27.237457367Z 	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
2019-01-04T14:02:27.237461597Z 	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
2019-01-04T14:02:27.237785145Z 	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
2019-01-04T14:02:27.237797467Z 	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
2019-01-04T14:02:27.237803320Z 	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
2019-01-04T14:02:27.237841314Z 	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
2019-01-04T14:02:27.237850959Z 	at org.broadinstitute.hellbender.Main.main(Main.java:289)
2019-01-04T14:02:27.282716927Z Using GATK jar /gatk/gatk-package-4.0.12.0-local.jar

@davidbenjamin
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@MikeWLloyd Could you provide the same data that I requested above from @byoo? If the data are public you could also share the whole unfiltered vcf.

@MikeWLloyd
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Unfortunately, these data are not public so I can not share them.

My Mutect2 runs were already split by chr. I've run one chr within a docker container built from docker pull broadinstitute/gatk using the command you provided above: gatk FilterMutectCalls -V chr1.vcf -O temp.vcf. That crashes out immediately (0.05 runtime) with the same error, and temp.vcf has the vcf header but nothing beyond the #CHROM line.

@davidbenjamin
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@MikeWLloyd Hmm, could you de-identifty your data by cutting out the header, contig, position, and allele fields and post the first few lines here? For example:

grep -v '#' unfiltered.vcf | cut -f 8,9,10,11 | head -n 100

This command yields the INFO and FORMAT fields alone.

@byoo
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byoo commented Jan 4, 2019

Sorry for late response. Here's a variant from my run causing the exception.

22      20067929        .       G       GC      .       .       DP=6;ECNT=1;MBQ=0,37;MFRL=0,141;MMQ=0,60;MPOS=15;POPAF=0.00;REF_BASES=CGCGAGGGGCGCCCGCGGGCG;RPA=3,4;RU=C;STR;TLOD=16.00 GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP 0/1:0,5:0.863:5:0,0:0,5:0.990,0.990,1.00:0.026,0.028,0.946

@MikeWLloyd
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Here are the first 100 lines.

DP=52;ECNT=7;MBQ=34,34;MFRL=193,222;MMQ=60,25;MPOS=24;POPAF=7.30;TLOD=7.50	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:47,3:0.077:50:26,2:21,1:0|1:47228_CATTGCTGTAAACTGCTCTGAG_C:47228:0.00,0.061,0.060:0.015,0.010,0.974
DP=46;ECNT=7;MBQ=27,28;MFRL=189,222;MMQ=60,25;MPOS=-2147483648;POPAF=7.30;TLOD=7.65	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:43,3:0.083:46:23,2:20,1:0|1:47228_CATTGCTGTAAACTGCTCTGAG_C:47228:0.00,0.061,0.065:0.018,9.594e-03,0.972
DP=52;ECNT=7;MBQ=33,37;MFRL=180,212;MMQ=50,25;MPOS=3;POPAF=4.79;TLOD=3.50	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:46,3:0.077:49:24,2:22,1:0.040,0.051,0.061:0.011,0.010,0.978
DP=60;ECNT=7;MBQ=34,36;MFRL=196,234;MMQ=60,25;MPOS=35;POPAF=3.24;TLOD=9.18	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:54,6:0.112:60:30,4:24,2:0.091,0.081,0.100:0.015,0.010,0.975
DP=55;ECNT=7;MBQ=27,35;MFRL=196,234;MMQ=60,25;MPOS=35;POPAF=Infinity;TLOD=9.51	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:48,6:0.124:54:29,4:19,2:0.091,0.091,0.111:0.034,7.667e-03,0.958
DP=49;ECNT=7;MBQ=34,36;MFRL=210,252;MMQ=60,25;MPOS=7;POPAF=Infinity;TLOD=5.42	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:39,4:0.109:43:21,2:18,2:0.061,0.081,0.093:0.043,6.665e-03,0.950
DP=33;ECNT=7;MBQ=36,34;MFRL=199,192;MMQ=60,22;MPOS=5;POPAF=Infinity;TLOD=3.17	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:28,3:0.119:31:16,1:12,2:0.00,0.101,0.097:0.108,5.601e-03,0.887
DP=33;ECNT=2;MBQ=28,33;MFRL=215,248;MMQ=48,24;MPOS=19;POPAF=4.68;TLOD=5.40	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:27,4:0.150:31:17,2:10,2:0|1:47476_G_A:47476:0.00,0.131,0.129:0.051,8.733e-03,0.940
DP=34;ECNT=2;MBQ=34,27;MFRL=218,248;MMQ=54,24;MPOS=24;POPAF=3.01;TLOD=24.33	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:23,10:0.308:33:13,6:10,4:0|1:47476_G_A:47476:0.263,0.283,0.303:0.022,0.018,0.959
DP=84;ECNT=4;MBQ=36,35;MFRL=204,169;MMQ=60,29;MPOS=35;POPAF=2.39;TLOD=7.20	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:78,5:0.070:83:30,3:48,2:0.00,0.061,0.060:0.036,4.734e-03,0.959
DP=114;ECNT=4;MBQ=36,36;MFRL=198,170;MMQ=60,27;MPOS=15;POPAF=2.83;TLOD=17.90	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:97,10:0.100:107:39,6:58,4:0.071,0.081,0.093:0.012,7.890e-03,0.981
DP=114;ECNT=4;MBQ=35,31;MFRL=199,231;MMQ=60,34;MPOS=6;POPAF=3.38;TLOD=8.50	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:104,6:0.062:110:44,3:60,3:0.040,0.040,0.055:6.996e-03,8.053e-03,0.985
DP=111;ECNT=4;MBQ=36,33;MFRL=202,172;MMQ=46,40;MPOS=17;POPAF=3.22;TLOD=16.78	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:99,9:0.090:108:46,6:53,3:0.020,0.081,0.083:0.425,1.547e-03,0.574
DP=84;ECNT=1;MBQ=34,36;MFRL=200,131;MMQ=40,25;MPOS=6;POPAF=Infinity;RPA=2,1;RU=TG;STR;TLOD=5.01	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:72,3:0.051:75:38,1:34,2:0.020,0.040,0.040:0.020,4.324e-03,0.976
DP=18;ECNT=2;MBQ=34,25;MFRL=226,199;MMQ=46,33;MPOS=21;POPAF=2.16;TLOD=13.24	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:14,4:0.250:18:10,3:4,1:0|1:48047_T_C:48047:0.212,0.172,0.222:0.020,0.021,0.959
DP=18;ECNT=2;MBQ=33,33;MFRL=227,199;MMQ=47,33;MPOS=19;POPAF=2.28;TLOD=13.36	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:13,4:0.263:17:10,3:3,1:0|1:48047_T_C:48047:0.222,0.182,0.235:0.020,0.022,0.958
DP=49;ECNT=1;MBQ=36,35;MFRL=186,214;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=73.15	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:27,22:0.451:49:11,13:16,9:0.444,0.404,0.449:0.025,0.021,0.954
DP=100;ECNT=1;MBQ=33,37;MFRL=190,219;MMQ=60,60;MPOS=25;POPAF=2.19;TLOD=136.40	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:53,40:0.432:93:18,14:35,26:0.394,0.414,0.430:0.018,0.022,0.961
DP=139;ECNT=1;MBQ=35,36;MFRL=212,204;MMQ=60,60;MPOS=28;POPAF=4.54;TLOD=244.66	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:60,70:0.538:130:26,42:34,28:0.535,0.374,0.538:8.981e-03,0.157,0.834
DP=3;ECNT=1;MBQ=36,36;MFRL=295,348;MMQ=60,60;MPOS=44;POPAF=7.30;RPA=4,5;RU=G;STR;TLOD=5.44	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:1,2:0.600:3:1,1:0,1:0.667,0.616,0.667:0.025,0.028,0.947
DP=11;ECNT=1;MBQ=27,27;MFRL=247,263;MMQ=60,60;MPOS=9;POPAF=7.30;RPA=16,15;RU=A;STR;TLOD=3.29	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:2,2:0.502:4:0,1:2,1:0.434,0.495,0.500:0.027,0.025,0.948
DP=2;ECNT=1;MBQ=0,35;MFRL=0,336;MMQ=0,60;MPOS=37;POPAF=7.30;TLOD=3.61	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,1:0.684:1:0,0:0,1:0.990,0.990,1.00:0.028,0.025,0.947
DP=28;ECNT=1;MBQ=35,37;MFRL=235,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=33.72	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:15,10:0.407:25:5,7:10,3:0.333,0.404,0.400:0.027,0.025,0.948
DP=32;ECNT=1;MBQ=36,32;MFRL=179,232;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=3.14	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:30,2:0.088:32:16,0:14,2:0.061,0.00,0.063:4.168e-03,0.151,0.845
DP=14;ECNT=1;MBQ=35,35;MFRL=165,236;MMQ=60,60;MPOS=17;POPAF=7.30;RPA=17,16;RU=A;STR;TLOD=5.63	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:3,4:0.564:7:0,0:3,4:0.515,0.576,0.571:0.029,0.025,0.947
DP=202;ECNT=1;MBQ=35,33;MFRL=189,195;MMQ=60,60;MPOS=17;POPAF=2.87;TLOD=281.74	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:106,85:0.446:191:45,38:61,47:0.404,0.434,0.445:0.029,0.010,0.961
DP=1;ECNT=1;MBQ=0,31;MFRL=0,162;MMQ=0,60;MPOS=28;POPAF=7.30;TLOD=3.28	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,1:0.667:1:0,1:0,0:0.990,0.990,1.00:0.025,0.028,0.947
DP=39;ECNT=3;MBQ=36,36;MFRL=202,209;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=5.69	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:12,3:0.228:15:9,2:3,1:0.202,0.121,0.200:0.022,0.024,0.955
DP=34;ECNT=3;MBQ=35,35;MFRL=232,203;MMQ=40,60;MPOS=15;POPAF=7.30;TLOD=5.47	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:5,8:0.587:13:5,6:0,2:0.616,0.566,0.615:0.025,0.029,0.946
DP=31;ECNT=3;MBQ=0,35;MFRL=0,196;MMQ=0,60;MPOS=6;POPAF=7.30;TLOD=5.11	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,29:0.968:29:0,18:0,11:0.990,0.990,1.00:0.025,0.030,0.945
DP=19;ECNT=1;MBQ=27,35;MFRL=224,257;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=29.72	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:9,9:0.500:18:4,7:5,2:0.434,0.505,0.500:0.034,0.021,0.944
DP=8;ECNT=1;MBQ=34,36;MFRL=309,300;MMQ=60,60;MPOS=21;POPAF=7.30;RPA=6,5;RU=C;STR;TLOD=10.20	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:3,4:0.556:7:2,2:1,2:0.556,0.535,0.571:0.029,0.024,0.948
DP=31;ECNT=1;MBQ=34,36;MFRL=233,215;MMQ=60,60;MPOS=24;POPAF=7.30;RPA=20,12;RU=A;STR;TLOD=59.29	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:10,15:0.596:25:2,6:8,9:0.576,0.576,0.600:0.021,0.028,0.951
DP=43;ECNT=2;MBQ=35,26;MFRL=248,231;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=89.69	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:19,23:0.545:42:11,12:8,11:0|1:3104904_C_G:3104904:0.505,0.545,0.548:0.024,0.028,0.948
DP=49;ECNT=2;MBQ=26,35;MFRL=248,228;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=93.16	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:19,24:0.556:43:11,12:8,12:0|1:3104904_C_G:3104904:0.515,0.556,0.558:0.024,0.028,0.948
DP=140;ECNT=1;MBQ=28,35;MFRL=202,173;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=235.64	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:64,70:0.522:134:27,38:37,32:0.485,0.515,0.522:0.025,0.016,0.959
DP=26;ECNT=1;MBQ=36,36;MFRL=269,254;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=43.81	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:13,13:0.500:26:7,7:6,6:0.465,0.475,0.500:0.047,0.015,0.938
DP=4;ECNT=1;MBQ=25,33;MFRL=247,214;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=10.85	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:1,3:0.667:4:1,2:0,1:0.747,0.707,0.750:0.025,0.029,0.946
DP=30;ECNT=1;MBQ=26,35;MFRL=237,268;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=30.68	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:18,10:0.367:28:11,5:7,5:0.313,0.354,0.357:0.019,0.032,0.949
DP=195;ECNT=1;MBQ=28,35;MFRL=199,187;MMQ=60,60;MPOS=25;POPAF=0.451;TLOD=320.43	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:86,97:0.529:183:50,51:36,46:0.525,0.505,0.530:0.014,0.024,0.962
DP=9;ECNT=1;MBQ=34,36;MFRL=298,329;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=17.08	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:4,5:0.546:9:2,3:2,2:0.556,0.495,0.556:0.025,0.029,0.946
DP=60;ECNT=2;MBQ=0,35;MFRL=0,200;MMQ=0,60;MPOS=20;POPAF=7.30;TLOD=244.09	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,59:0.984:59:0,34:0,25:0.990,0.990,1.00:0.030,0.025,0.945
DP=70;ECNT=2;MBQ=27,34;MFRL=195,194;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=115.01	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:33,36:0.524:69:19,17:14,19:0.465,0.525,0.522:0.044,0.019,0.938
DP=113;ECNT=1;MBQ=36,36;MFRL=182,191;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=168.56	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:57,51:0.472:108:27,22:30,29:0.455,0.444,0.472:0.030,0.013,0.957
DP=15;ECNT=2;MBQ=0,33;MFRL=0,237;MMQ=0,60;MPOS=17;POPAF=7.30;RPA=3,2;RU=C;STR;TLOD=44.57	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,13:0.937:13:0,9:0,4:0.990,0.990,1.00:0.025,0.030,0.945
DP=7;ECNT=2;MBQ=0,37;MFRL=0,251;MMQ=0,60;MPOS=18;POPAF=7.30;TLOD=30.60	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,7:0.889:7:0,4:0,3:0.990,0.990,1.00:0.025,0.030,0.945
DP=175;ECNT=1;MBQ=27,34;MFRL=201,192;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=231.52	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:89,74:0.455:163:48,36:41,38:0.424,0.444,0.454:0.020,0.019,0.961
DP=176;ECNT=1;MBQ=26,34;MFRL=187,202;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=252.36	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:89,79:0.470:168:46,33:43,46:0.444,0.465,0.470:0.014,0.025,0.960
DP=7;ECNT=1;MBQ=32,36;MFRL=242,319;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=14.55	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:1,4:0.722:5:1,1:0,3:0.798,0.768,0.800:0.025,0.029,0.946
DP=126;ECNT=1;MBQ=35,35;MFRL=202,183;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=202.43	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:58,61:0.512:119:23,27:35,34:0.465,0.515,0.513:0.030,0.020,0.950
DP=22;ECNT=1;MBQ=35,33;MFRL=270,252;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=30.65	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:11,10:0.478:21:5,6:6,4:0.475,0.414,0.476:0.025,0.028,0.947
DP=37;ECNT=1;MBQ=35,36;MFRL=210,219;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=69.66	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:16,21:0.562:37:11,8:5,13:0.525,0.566,0.568:0.024,0.028,0.948
DP=282;ECNT=1;MBQ=35,36;MFRL=190,177;MMQ=60,60;MPOS=21;POPAF=2.42;TLOD=483.00	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:129,142:0.524:271:62,73:67,69:0.515,0.505,0.524:9.502e-03,0.029,0.962
DP=102;ECNT=1;MBQ=36,36;MFRL=223,207;MMQ=60,60;MPOS=21;POPAF=2.42;TLOD=182.44	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:44,53:0.545:97:28,26:16,27:0.505,0.545,0.546:0.027,0.022,0.951
DP=448;ECNT=1;MBQ=29,33;MFRL=183,186;MMQ=60,60;MPOS=23;POPAF=2.40;TLOD=652.14	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:220,207:0.485:427:96,96:124,111:0.444,0.475,0.485:0.081,4.923e-03,0.914
DP=213;ECNT=1;MBQ=34,35;MFRL=208,199;MMQ=60,60;MPOS=18;POPAF=2.42;TLOD=314.62	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:109,95:0.466:204:49,50:60,45:0.404,0.455,0.466:0.204,4.633e-03,0.791
DP=39;ECNT=1;MBQ=35,34;MFRL=214,190;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=64.80	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:19,20:0.512:39:12,11:7,9:0.465,0.505,0.513:0.025,0.023,0.952
DP=25;ECNT=1;MBQ=37,36;MFRL=281,282;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=45.52	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:11,13:0.539:24:6,8:5,5:0.505,0.535,0.542:0.020,0.032,0.947
DP=60;ECNT=1;MBQ=0,36;MFRL=0,190;MMQ=0,60;MPOS=27;POPAF=0.515;TLOD=240.39	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,59:0.984:59:0,30:0,29:0.990,0.990,1.00:0.027,0.027,0.946
DP=26;ECNT=1;MBQ=0,36;MFRL=0,223;MMQ=0,60;MPOS=24;POPAF=7.30;TLOD=95.06	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,24:0.963:24:0,15:0,9:0.990,0.990,1.00:0.025,0.029,0.946
DP=2;ECNT=1;MBQ=0,33;MFRL=0,358;MMQ=0,60;MPOS=31;POPAF=7.30;TLOD=7.08	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,2:0.750:2:0,0:0,2:0.990,0.990,1.00:0.029,0.025,0.946
DP=10;ECNT=1;MBQ=35,34;MFRL=259,295;MMQ=50,47;MPOS=14;POPAF=7.30;TLOD=19.06	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:5,5:0.500:10:3,2:2,3:0.434,0.495,0.500:0.028,0.025,0.947
DP=3;ECNT=5;MBQ=0,33;MFRL=0,380;MMQ=0,27;MPOS=18;POPAF=0.194;TLOD=11.57	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,3:0.800:3:0,2:0,1:0.990,0.990,1.00:0.030,0.025,0.945
DP=4;ECNT=5;MBQ=0,34;MFRL=0,347;MMQ=0,34;MPOS=33;POPAF=0.209;TLOD=17.30	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:0,4:0.833:4:0,3:0,1:0|1:4975982_C_T:4975982:0.990,0.990,1.00:0.030,0.025,0.945
DP=4;ECNT=5;MBQ=0,37;MFRL=0,347;MMQ=0,34;MPOS=33;POPAF=7.30;TLOD=17.30	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SAAF:SAPP	0|1:0,4:0.833:4:0,3:0,1:0|1:4975982_C_T:4975982:0.990,0.990,1.00:0.030,0.025,0.945
DP=4;ECNT=5;MBQ=0,28;MFRL=0,347;MMQ=0,34;MPOS=31;POPAF=7.30;TLOD=14.85	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,4:0.833:4:0,3:0,1:0.990,0.990,1.00:0.030,0.025,0.945
DP=3;ECNT=5;MBQ=33,33;MFRL=380,342;MMQ=27,34;MPOS=21;POPAF=7.30;TLOD=5.87	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:1,2:0.600:3:1,2:0,0:0.616,0.667,0.667:0.028,0.025,0.947
DP=6;ECNT=1;MBQ=36,32;MFRL=259,252;MMQ=55,49;MPOS=20;POPAF=7.30;TLOD=8.25	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:2,3:0.573:5:1,2:1,1:0.596,0.545,0.600:0.025,0.029,0.947
DP=1;ECNT=1;MBQ=0,36;MFRL=0,330;MMQ=0,47;MPOS=3;POPAF=7.30;TLOD=3.77	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,1:0.667:1:0,0:0,1:0.990,0.990,1.00:0.028,0.025,0.947
DP=31;ECNT=1;MBQ=35,34;MFRL=224,205;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=43.92	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:16,14:0.469:30:9,8:7,6:0.465,0.394,0.467:0.016,0.043,0.941
DP=1;ECNT=1;MBQ=0,36;MFRL=0,221;MMQ=0,60;MPOS=30;POPAF=7.30;TLOD=3.78	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,1:0.667:1:0,1:0,0:0.990,0.990,1.00:0.028,0.025,0.947
DP=116;ECNT=1;MBQ=37,34;MFRL=203,223;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=186.78	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:55,58:0.513:113:26,32:29,26:0.495,0.485,0.513:0.037,0.013,0.949
DP=6;ECNT=1;MBQ=0,36;MFRL=0,313;MMQ=0,60;MPOS=34;POPAF=7.30;TLOD=23.17	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,6:0.875:6:0,3:0,3:0.990,0.990,1.00:0.025,0.029,0.946
DP=77;ECNT=1;MBQ=27,35;MFRL=198,214;MMQ=60,60;MPOS=26;POPAF=2.26;TLOD=102.64	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:40,32:0.446:72:27,16:13,16:0.444,0.384,0.444:0.021,0.034,0.945
DP=368;ECNT=1;MBQ=36,34;MFRL=183,189;MMQ=60,60;MPOS=26;POPAF=3.02;TLOD=559.31	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:177,175:0.497:352:96,81:81,94:0.485,0.485,0.497:0.017,0.012,0.971
DP=3;ECNT=1;MBQ=0,33;MFRL=0,354;MMQ=0,60;MPOS=10;POPAF=7.30;TLOD=10.48	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,3:0.800:3:0,0:0,3:0.990,0.990,1.00:0.030,0.025,0.945
DP=22;ECNT=1;MBQ=0,24;MFRL=0,215;MMQ=0,60;MPOS=19;POPAF=7.30;TLOD=62.65	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,22:0.958:22:0,14:0,8:0.990,0.990,1.00:0.029,0.025,0.946
DP=69;ECNT=1;MBQ=36,36;MFRL=227,251;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=120.26	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:29,35:0.545:64:13,16:16,19:0.515,0.535,0.547:0.019,0.027,0.955
DP=43;ECNT=1;MBQ=32,32;MFRL=196,208;MMQ=60,60;MPOS=31;POPAF=7.30;RPA=9,10;RU=A;STR;TLOD=44.02	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:20,20:0.500:40:8,11:12,9:0.495,0.455,0.500:0.020,0.028,0.952
DP=5;ECNT=1;MBQ=28,34;MFRL=214,268;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=6.24	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:2,2:0.500:4:1,1:1,1:0.434,0.495,0.500:0.027,0.025,0.948
DP=2;ECNT=1;MBQ=32,35;MFRL=158,142;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=3.20	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:1,1:0.500:2:0,0:1,1:0.495,0.424,0.500:0.025,0.027,0.948
DP=1;ECNT=1;MBQ=0,35;MFRL=0,288;MMQ=0,60;MPOS=4;POPAF=7.30;TLOD=3.17	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,1:0.667:1:0,1:0,0:0.990,0.990,1.00:0.025,0.028,0.947
DP=3;ECNT=1;MBQ=0,35;MFRL=0,218;MMQ=0,60;MPOS=21;POPAF=7.30;TLOD=7.43	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,2:0.764:2:0,1:0,1:0.990,0.990,1.00:0.029,0.025,0.946
DP=48;ECNT=1;MBQ=35,35;MFRL=240,269;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=58.70	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:27,18:0.404:45:12,8:15,10:0.374,0.374,0.400:0.012,0.053,0.935
DP=151;ECNT=1;MBQ=35,35;MFRL=195,187;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=263.51	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:70,68:0.493:138:37,34:33,34:0.475,0.475,0.493:0.019,0.017,0.964
DP=40;ECNT=1;MBQ=36,35;MFRL=236,177;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=51.51	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:21,16:0.436:37:6,5:15,11:0.424,0.384,0.432:0.025,0.022,0.953
DP=4;ECNT=1;MBQ=0,33;MFRL=0,285;MMQ=0,60;MPOS=28;POPAF=7.30;RPA=7,8;RU=T;STR;TLOD=11.46	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,4:0.833:4:0,1:0,3:0.990,0.990,1.00:0.030,0.025,0.945
DP=66;ECNT=1;MBQ=37,35;MFRL=184,196;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=87.05	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:36,27:0.431:63:18,12:18,15:0.414,0.394,0.429:0.031,0.017,0.953
DP=16;ECNT=1;MBQ=0,37;MFRL=0,243;MMQ=0,60;MPOS=21;POPAF=7.30;RPA=8,9;RU=A;STR;TLOD=36.56	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,13:0.938:13:0,9:0,4:0.990,0.990,1.00:0.025,0.030,0.945
DP=98;ECNT=1;MBQ=33,33;MFRL=181,186;MMQ=60,60;MPOS=24;POPAF=7.30;RPA=2,1;RU=TCT;STR;TLOD=139.10	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:48,37:0.437:85:20,19:28,18:0.434,0.354,0.435:0.013,0.058,0.929
DP=27;ECNT=1;MBQ=0,32;MFRL=0,229;MMQ=0,40;MPOS=22;POPAF=7.30;RPA=23,25;RU=T;STR;TLOD=12.42	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,6:0.908:6:0,3:0,3:0.990,0.990,1.00:0.025,0.030,0.945
DP=5;ECNT=1;MBQ=36,35;MFRL=247,262;MMQ=60,60;MPOS=14;POPAF=7.30;RPA=18,17;RU=A;STR;TLOD=3.12	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:2,2:0.501:4:2,0:0,2:0.434,0.495,0.500:0.027,0.025,0.948
DP=80;ECNT=1;MBQ=0,35;MFRL=0,186;MMQ=0,60;MPOS=22;POPAF=7.30;TLOD=295.23	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:0,74:0.987:74:0,27:0,47:0.990,0.990,1.00:0.028,0.026,0.946
DP=55;ECNT=1;MBQ=31,29,29,28;MFRL=176,186,209,229;MMQ=60,60,60,60;MPOS=30,26,20;POPAF=0.467,7.30,0.867;RPA=17,18,19,20;RU=A;STR;TLOD=14.26,13.49,4.01	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1/2/3:4,10,10,4:0.340,0.359,0.156:28:2,3,3,1:2,7,7,3:0.717,0.677,0.714:0.025,0.030,0.946
DP=20;ECNT=1;MBQ=35,27;MFRL=152,219;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=34.91	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:7,13:0.634:20:3,10:4,3:0.636,0.616,0.650:0.022,0.030,0.949
DP=35;ECNT=1;MBQ=34,36;MFRL=204,212;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=23.57	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:27,8:0.243:35:12,6:15,2:0.232,0.152,0.229:0.017,0.032,0.952
DP=9;ECNT=1;MBQ=36,33;MFRL=305,331;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=15.78	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:4,5:0.545:9:2,1:2,4:0.495,0.556,0.556:0.029,0.025,0.946
DP=48;ECNT=1;MBQ=36,34;MFRL=215,229;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=81.26	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:22,25:0.531:47:12,10:10,15:0.475,0.535,0.532:0.035,0.021,0.944
DP=106;ECNT=1;MBQ=33,34;MFRL=236,234;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=150.52	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:55,47:0.462:102:31,20:24,27:0.414,0.455,0.461:0.025,0.025,0.950
DP=12;ECNT=1;MBQ=35,32;MFRL=233,222;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=22.11	GT:AD:AF:DP:F1R2:F2R1:SAAF:SAPP	0/1:3,7:0.669:10:1,4:2,3:0.687,0.677,0.700:0.023,0.030,0.947

@davidbenjamin
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@byoo @MikeWLloyd Thanks very much! I will fix this ASAP.

@davidbenjamin davidbenjamin mentioned this issue Jan 6, 2019
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@davidbenjamin
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@byoo @MikeWLloyd I reproduced your errors and fixed them, at least on my laptop, in PR #5563. Thank you for your help, and please don't hesitate to speak up if the bug remains for you once this PR goes in.

@bounlu
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bounlu commented Jan 6, 2019 •
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I just got the same error:

Using GATK jar /software/anaconda2/share/gatk4-4.0.12.0-0/gatk-package-4.0.12.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx16G -jar /software/anaconda2/share/gatk4-4.0.12.0-0/gatk-package-4.0.12.0-local.jar FilterMutectCalls -V tumor-vs-normal.mutect.temp1.vcf -O tumor-vs-normal.mutect.temp2.vcf
22:58:25.052 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/software/anaconda2/share/gatk4-4.0.12.0-0/gatk-package-4.0.12.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
22:58:26.911 INFO  FilterMutectCalls - ------------------------------------------------------------
22:58:26.912 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.0.12.0
22:58:26.912 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
22:58:26.912 INFO  FilterMutectCalls - Executing as www-data@SpongeBob on Linux v4.15.0-39-generic amd64
22:58:26.912 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
22:58:26.912 INFO  FilterMutectCalls - Start Date/Time: January 6, 2019 10:58:24 PM SGT
22:58:26.913 INFO  FilterMutectCalls - ------------------------------------------------------------
22:58:26.913 INFO  FilterMutectCalls - ------------------------------------------------------------
22:58:26.913 INFO  FilterMutectCalls - HTSJDK Version: 2.18.1
22:58:26.913 INFO  FilterMutectCalls - Picard Version: 2.18.16
22:58:26.913 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:58:26.913 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:58:26.913 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:58:26.913 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:58:26.914 INFO  FilterMutectCalls - Deflater: IntelDeflater
22:58:26.914 INFO  FilterMutectCalls - Inflater: IntelInflater
22:58:26.914 INFO  FilterMutectCalls - GCS max retries/reopens: 20
22:58:26.914 INFO  FilterMutectCalls - Requester pays: disabled
22:58:26.914 INFO  FilterMutectCalls - Initializing engine
22:58:27.401 INFO  FeatureManager - Using codec VCFCodec to read file file://tumor-vs-normal.mutect.temp1.vcf
22:58:27.518 INFO  FilterMutectCalls - Done initializing engine
22:58:27.570 INFO  ProgressMeter - Starting traversal
22:58:27.571 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
22:58:27.571 INFO  FilterMutectCalls - Starting first pass through the variants
22:58:28.484 INFO  FilterMutectCalls - Shutting down engine
[January 6, 2019 10:58:28 PM SGT] org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=2141192192
java.lang.IllegalArgumentException: errorRateLog10 must be good probability but got NaN
	at org.broadinstitute.hellbender.utils.QualityUtils.phredScaleLog10ErrorRate(QualityUtils.java:321)
	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.lambda$applyGermlineVariantFilter$10(Mutect2FilteringEngine.java:207)
	at java.util.stream.DoublePipeline$3$1.accept(DoublePipeline.java:231)
	at java.util.Spliterators$DoubleArraySpliterator.forEachRemaining(Spliterators.java:1198)
	at java.util.Spliterator$OfDouble.forEachRemaining(Spliterator.java:822)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
	at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
	at java.util.stream.IntPipeline.toArray(IntPipeline.java:502)
	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.applyGermlineVariantFilter(Mutect2FilteringEngine.java:207)
	at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.calculateFilters(Mutect2FilteringEngine.java:436)
	at org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls.firstPassApply(FilterMutectCalls.java:120)
	at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.lambda$traverseVariants$0(TwoPassVariantWalker.java:76)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
	at java.util.Iterator.forEachRemaining(Iterator.java:116)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
	at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverseVariants(TwoPassVariantWalker.java:74)
	at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverse(TwoPassVariantWalker.java:27)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	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)

@chapmanb chapmanb mentioned this issue Jan 19, 2019
Closed
@igordot igordot mentioned this issue Mar 20, 2019
Closed
@sahilseth
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Has this been fixed with 4.1.1.0?

gatk-4.1.1.0

I think, its the same bug?

# java.lang.IllegalArgumentException: errorRateLog10 must be good probability but got NaN

CONTQ=93;DP=393;ECNT=1;GERMQ=93;MBQ=22,14;MFRL=0,0;MMQ=81,79;MPOS=17;NALOD=-2.519e+01;NLOD=17.32;PON;POPAF=6.00;RPA=2,1;RU=C;SEQQ=93;STR;STRANDQ=6;STRQ=93;TLOD=29.34	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:204,13:0.064:217:176,2:1,0:1,203,0,13	0/1:161,15:0.086:176:115,3:1,0:1,160,0,15
CONTQ=76;DP=44;ECNT=1;GERMQ=93;MBQ=25,14;MFRL=0,0;MMQ=92,88;MPOS=52;NALOD=1.38;NLOD=6.90;POPAF=6.00;SEQQ=56;STRANDQ=1;TLOD=7.00	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:23,0:0.040:23:7,0:12,0:13,10,0,0	0/1:18,3:0.174:21:8,0:7,0:9,9,3,0
CONTQ=61;DP=40;ECNT=1;GERMQ=89;MBQ=27,25;MFRL=0,0;MMQ=93,87;MPOS=39;NALOD=-1.380e+00;NLOD=2.27;POPAF=6.00;SEQQ=33;STRANDQ=3;TLOD=4.55	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:20,1:0.087:21:12,1:6,0:7,13,0,1	0/1:17,2:0.143:19:12,2:4,0:5,12,0,2
CONTQ=82;DP=92;ECNT=1;GERMQ=93;MBQ=23,23;MFRL=0,0;MMQ=94,92;MPOS=51;NALOD=-1.699e+00;NLOD=8.01;PON;POPAF=6.00;RPA=4,5;RU=C;SEQQ=35;STR;STRANDQ=25;STRQ=93;TLOD=4.59	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:46,2:0.060:48:32,2:10,0:12,34,0,2	0/1:40,4:0.104:44:27,3:10,0:13,27,1,3
CONTQ=82;DP=199;ECNT=1;GERMQ=93;MBQ=27,20;MFRL=0,0;MMQ=91,91;MPOS=56;NALOD=-1.064e+00;NLOD=26.51;PON;POPAF=6.00;RPA=4,3;RU=T;SEQQ=66;STR;STRANDQ=1;STRQ=93;TLOD=7.68	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:109,2:0.026:111:102,1:4,1:4,105,1,1	0/1:83,5:0.066:88:77,1:4,2:5,78,4,1
CONTQ=93;DP=48;ECNT=1;GERMQ=1;MBQ=22,22,23;MFRL=0,0,0;MMQ=90,88,86;MPOS=44,29;NALOD=-6.835e+01,1.26;NLOD=-6.813e+01,9.19;PON;POPAF=6.00,6.00;RPA=3,2,4;RU=G;SEQQ=93;STR;STRANDQ=79;STRQ=93;TLOD=21.02,4.38	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:12,22,0:0.622,0.027:34:4,0,0:7,15,0:8,4,22,0	0/1/2:5,7,2:0.471,0.176:14:1,0,2:3,3,0:4,1,7,2
CONTQ=57;DP=68;ECNT=1;GERMQ=93;MBQ=24,23;MFRL=0,0;MMQ=90,89;MPOS=50;NALOD=1.58;NLOD=11.14;POPAF=6.00;SEQQ=28;STRANDQ=6;TLOD=3.96	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:37,0:0.025:37:34,0:1,0:1,36,0,0	0/1:28,2:0.094:30:23,1:1,0:1,27,0,2
CONTQ=49;DP=105;ECNT=1;GERMQ=93;MBQ=24,19;MFRL=0,0;MMQ=92,87;MPOS=33;NALOD=1.74;NLOD=15.95;POPAF=6.00;RPA=2,1;RU=G;SEQQ=22;STR;STRANDQ=19;STRQ=93;TLOD=3.37	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:53,0:0.018:53:33,0:18,0:19,34,0,0	0/1:49,2:0.057:51:31,1:14,0:16,33,1,1
CONTQ=93;DP=138;ECNT=1;GERMQ=93;MBQ=23,9;MFRL=0,0;MMQ=84,91;MPOS=22;NALOD=1.67;NLOD=16.08;POPAF=6.00;SEQQ=22;STRANDQ=1;TLOD=3.57	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:63,4:0.021:67:39,0:9,0:23,40,4,0	0/1:61,10:0.092:71:40,0:6,0:19,42,10,0
CONTQ=54;DP=68;ECNT=1;GERMQ=93;MBQ=23,14;MFRL=0,0;MMQ=85,77;MPOS=11;NALOD=-5.165e-02;NLOD=6.28;POPAF=6.00;SEQQ=41;STRANDQ=4;TLOD=7.17	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:37,2:0.062:39:24,0:4,0:7,30,0,2	0/1:26,3:0.132:29:16,2:0,0:3,23,0,3
CONTQ=73;DP=69;ECNT=1;GERMQ=93;MBQ=25,22;MFRL=0,0;MMQ=90,76;MPOS=55;NALOD=-7.771e-02;NLOD=8.47;PON;POPAF=6.00;RPA=5,4;RU=G;SEQQ=36;STR;STRANDQ=2;STRQ=93;TLOD=4.75	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:38,1:0.048:39:24,1:12,0:12,26,0,1	0/1:26,3:0.128:29:15,3:9,0:10,16,0,3
CONTQ=73;DP=153;ECNT=1;GERMQ=93;MBQ=24,16;MFRL=0,0;MMQ=90,71;MPOS=8;NALOD=-1.984e+00;NLOD=17.26;POPAF=6.00;RPA=2,1;RU=C;SEQQ=59;STR;STRANDQ=4;STRQ=93;TLOD=6.98	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:80,2:0.036:82:60,0:11,0:16,64,0,2	0/1:67,4:0.068:71:49,1:9,0:12,55,0,4
CONTQ=57;DP=61;ECNT=2;GERMQ=93;MBQ=27,17;MFRL=0,0;MMQ=60,90;MPOS=29;NALOD=1.51;NLOD=9.33;PON;POPAF=6.00;RPA=2,1;RU=G;SEQQ=22;STR;STRANDQ=1;STRQ=93;TLOD=3.35	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:31,0:0.030:31:26,0:5,0:5,26,0,0	0/1:27,2:0.096:29:23,0:2,1:4,23,2,0
CONTQ=73;DP=60;ECNT=2;GERMQ=93;MBQ=26,14;MFRL=0,0;MMQ=61,74;MPOS=-1073741811;NALOD=-6.840e-01;NLOD=5.65;PON;POPAF=6.00;RPA=2,1;RU=T;SEQQ=64;STR;STRANDQ=14;STRQ=93;TLOD=7.64	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:30,1:0.060:31:24,0:5,0:5,25,0,1	0/1:26,3:0.129:29:21,0:1,1:4,22,2,1
CONTQ=74;DP=56;ECNT=1;GERMQ=93;MBQ=25,12;MFRL=0,0;MMQ=94,89;MPOS=23;NALOD=-9.066e-01;NLOD=4.33;PON;POPAF=6.00;SEQQ=45;STRANDQ=5;TLOD=5.78	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:26,1:0.068:27:19,0:4,0:4,22,0,1	0/1:24,3:0.139:27:17,0:1,0:1,23,0,3
CONTQ=54;DP=198;ECNT=2;GERMQ=93;MBQ=27,13;MFRL=0,0;MMQ=89,54;MPOS=68;NALOD=2.07;NLOD=35.20;POPAF=6.00;SEQQ=33;STRANDQ=10;TLOD=4.62	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:117,0:8.405e-03:117:113,0:1,0:1,116,0,0	0/1:78,3:0.048:81:71,0:3,0:3,75,0,3
CONTQ=62;DP=40;ECNT=2;GERMQ=93;MBQ=27,19;MFRL=0,0;MMQ=74,86;MPOS=80;NALOD=1.40;NLOD=7.22;POPAF=6.00;SEQQ=32;STRANDQ=4;TLOD=4.55	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:24,0:0.038:24:24,0:0,0:0,24,0,0	0/1:14,2:0.167:16:12,1:1,0:2,12,0,2
CONTQ=81;DP=100;ECNT=3;GERMQ=93;MBQ=21,18;MFRL=0,0;MMQ=93,91;MPOS=21;NALOD=-4.610e+00;NLOD=4.71;PON;POPAF=6.00;RPA=3,2;RU=G;SEQQ=62;STR;STRANDQ=4;STRQ=93;TLOD=7.21	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:48,3:0.075:51:33,1:5,0:5,43,0,3	0/1:45,4:0.098:49:23,1:6,0:6,39,0,4
CONTQ=62;DP=126;ECNT=3;GERMQ=93;MBQ=25,13;MFRL=0,0;MMQ=93,89;MPOS=29;NALOD=-2.781e+00;NLOD=11.84;POPAF=6.00;SEQQ=21;STRANDQ=27;TLOD=3.20	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:63,2:0.045:65:53,0:4,0:4,59,0,2	0/1:56,3:0.057:59:46,0:4,0:4,52,1,2
CONTQ=73;DP=138;ECNT=3;GERMQ=93;MBQ=26,11;MFRL=0,0;MMQ=93,81;MPOS=9;NALOD=1.54;NLOD=19.91;PON;POPAF=6.00;SEQQ=23;STRANDQ=6;TLOD=3.32	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:67,1:0.015:68:58,0:4,0:4,63,0,1	0/1:65,4:0.057:69:55,0:6,0:6,59,0,4
CONTQ=61;DP=35;ECNT=2;GERMQ=93;MBQ=26,22;MFRL=0,0;MMQ=92,87;MPOS=14;NALOD=1.26;NLOD=5.12;POPAF=6.00;RPA=1,2;RU=G;SEQQ=26;STR;STRANDQ=1;STRQ=93;TLOD=3.93	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:17,0:0.053:17:2,0:12,0:12,5,0,0	0/1:16,2:0.150:18:5,2:9,0:9,7,0,2
CONTQ=78;DP=35;ECNT=2;GERMQ=93;MBQ=22,14;MFRL=0,0;MMQ=93,87;MPOS=57;NALOD=1.26;NLOD=5.12;POPAF=6.00;RPA=2,1;RU=C;SEQQ=36;STR;STRANDQ=1;STRQ=93;TLOD=5.18	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:17,0:0.053:17:4,0:9,0:12,5,0,0	0/1:15,3:0.197:18:3,1:7,0:9,6,0,3
CONTQ=70;DP=85;ECNT=1;GERMQ=93;MBQ=26,15;MFRL=0,0;MMQ=94,80;MPOS=14;NALOD=-2.038e+00;NLOD=7.66;PON;POPAF=6.00;SEQQ=18;STRANDQ=1;TLOD=5.34	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:54,5:0.083:59:23,1:31,0:31,23,0,5	0/1:22,4:0.173:26:10,2:12,0:12,10,0,4
CONTQ=93;DP=119;ECNT=1;GERMQ=93;MBQ=26,18;MFRL=0,0;MMQ=96,92;MPOS=36;NALOD=-6.682e+00;NLOD=6.74;PON;POPAF=6.00;RPA=6,5;RU=G;SEQQ=56;STR;STRANDQ=36;STRQ=93;TLOD=6.82	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:70,5:0.077:75:30,0:39,2:39,31,3,2	0/1:38,5:0.133:43:10,1:27,2:27,11,2,3
CONTQ=93;DP=219;ECNT=1;GERMQ=93;MBQ=23,20;MFRL=0,0;MMQ=86,74;MPOS=64;NALOD=-2.111e+01;NLOD=3.73;PON;POPAF=6.00;RPA=2,3;RU=G;SEQQ=93;STR;STRANDQ=4;STRQ=93;TLOD=11.53	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:128,11:0.079:139:93,8:9,0:14,114,0,11	0/1:74,6:0.085:80:48,5:7,0:10,64,0,6
CONTQ=51;DP=103;ECNT=1;GERMQ=93;MBQ=27,23;MFRL=0,0;MMQ=92,84;MPOS=58;NALOD=-6.441e+00;NLOD=3.09;PON;POPAF=6.00;RPA=4,3;RU=A;SEQQ=21;STR;STRANDQ=4;STRQ=93;TLOD=3.23	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:52,4:0.086:56:26,1:25,3:26,26,3,1	0/1:44,2:0.062:46:30,2:13,0:13,31,0,2
CONTQ=3;DP=175;ECNT=1;GERMQ=93;MBQ=21,13;MFRL=0,0;MMQ=87,83;MPOS=10;NALOD=-3.940e+00;NLOD=9.57;PON;POPAF=6.00;RPA=5,2;RU=G;SEQQ=1;STR;STRANDQ=1;STRQ=93;TLOD=3.26	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:68,4:0.061:72:10,1:22,0:22,46,0,4	0/1:33,3:0.099:36:0,2:18,0:19,14,0,3
CONTQ=66;DP=18;ECNT=3;GERMQ=68;MBQ=23,16;MFRL=0,0;MMQ=90,82;MPOS=66;NALOD=1.04;NLOD=3.01;POPAF=6.00;SEQQ=47;STRANDQ=5;TLOD=6.60	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:10,0:0.083:10:5,0:4,0:5,5,0,0	0/1:6,2:0.300:8:2,0:4,1:4,2,2,0
CONTQ=65;DP=24;ECNT=3;GERMQ=67;MBQ=27,21;MFRL=0,0;MMQ=89,81;MPOS=35;NALOD=0.677;NLOD=2.43;POPAF=6.00;RPA=1,2;RU=C;SEQQ=46;STR;STRANDQ=3;STRQ=93;TLOD=6.29	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|0:12,1:0.116:13:5,0:5,0:0|1:908498_G_GC:908498:5,7,0,1	0|1:8,2:0.249:10:2,0:4,2:0|1:908498_G_GC:908498:4,4,2,0
CONTQ=65;DP=26;ECNT=3;GERMQ=67;MBQ=27,18;MFRL=0,0;MMQ=89,81;MPOS=32;NALOD=0.692;NLOD=2.44;POPAF=6.00;RPA=2,1;RU=C;SEQQ=46;STR;STRANDQ=3;STRQ=93;TLOD=6.27	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|0:12,1:0.115:13:5,0:5,0:0|1:908498_G_GC:908498:5,7,0,1	0|1:8,2:0.247:10:2,0:4,1:0|1:908498_G_GC:908498:4,4,2,0
CONTQ=93;DP=44;ECNT=1;GERMQ=76;MBQ=26,21;MFRL=0,0;MMQ=93,84;MPOS=35;NALOD=-6.183e-01;NLOD=3.99;PON;POPAF=6.00;RPA=4,3;RU=T;SEQQ=93;STR;STRANDQ=20;STRQ=93;TLOD=13.03	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:24,1:0.074:25:4,0:19,0:19,5,1,0	0/1:13,5:0.300:18:2,3:11,1:11,2,1,4
CONTQ=61;DP=40;ECNT=2;GERMQ=93;MBQ=26,13;MFRL=0,0;MMQ=92,70;MPOS=20;NALOD=1.34;NLOD=6.28;PON;POPAF=6.00;RPA=2,1;RU=A;SEQQ=23;STR;STRANDQ=1;STRQ=93;TLOD=3.61	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:21,0:0.044:21:12,0:4,0:6,15,0,0	0/1:17,2:0.143:19:9,0:4,0:5,12,2,0
CONTQ=77;DP=40;ECNT=2;GERMQ=93;MBQ=26,11;MFRL=0,0;MMQ=92,74;MPOS=1;NALOD=1.33;NLOD=6.02;PON;POPAF=6.00;RPA=2,1;RU=G;SEQQ=33;STR;STRANDQ=1;STRQ=93;TLOD=4.80	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:20,0:0.045:20:14,0:3,0:5,15,0,0	0/1:16,3:0.173:19:10,0:3,0:4,12,3,0
CONTQ=71;DP=103;ECNT=1;GERMQ=93;MBQ=27,21;MFRL=0,0;MMQ=93,90;MPOS=30;NALOD=0.119;NLOD=15.47;PON;POPAF=6.00;RPA=2,3;RU=C;SEQQ=41;STR;STRANDQ=1;STRQ=93;TLOD=5.19	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:62,1:0.030:63:51,0:7,0:11,51,1,0	0/1:31,3:0.111:34:24,0:6,3:7,24,3,0
CONTQ=54;DP=83;ECNT=3;GERMQ=93;MBQ=23,16;MFRL=0,0;MMQ=94,93;MPOS=36;NALOD=-5.794e+00;NLOD=2.42;PON;POPAF=6.00;SEQQ=24;STRANDQ=3;TLOD=3.48	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:44,3:0.082:47:26,1:11,0:11,33,0,3	0/1:34,2:0.079:36:16,1:12,0:12,22,0,2
CONTQ=58;DP=65;ECNT=3;GERMQ=93;MBQ=27,20;MFRL=0,0;MMQ=96,88;MPOS=57;NALOD=1.59;NLOD=11.44;PON;POPAF=6.00;SEQQ=34;STRANDQ=3;TLOD=4.55	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:38,0:0.025:38:26,0:11,0:11,27,0,0	0/1:25,2:0.103:27:17,1:6,0:7,18,0,2
CONTQ=57;DP=69;ECNT=3;GERMQ=93;MBQ=27,12;MFRL=0,0;MMQ=96,84;MPOS=29;NALOD=1.61;NLOD=12.04;POPAF=6.00;SEQQ=24;STRANDQ=4;TLOD=3.54	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:40,0:0.024:40:28,0:11,0:11,29,0,0	0/1:27,2:0.097:29:20,0:7,0:7,20,0,2
CONTQ=66;DP=113;ECNT=1;GERMQ=93;MBQ=27,8;MFRL=0,0;MMQ=89,90;MPOS=14;NALOD=-9.745e-01;NLOD=13.20;POPAF=6.00;RPA=3,2;RU=T;SEQQ=26;STR;STRANDQ=1;STRQ=93;TLOD=3.66	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:62,2:0.044:64:52,0:0,0:10,52,2,0	0/1:44,3:0.081:47:40,0:1,0:4,40,3,0
CONTQ=72;DP=58;ECNT=2;GERMQ=93;MBQ=23,14;MFRL=0,0;MMQ=96,79;MPOS=19;NALOD=-5.874e-01;NLOD=4.93;POPAF=6.00;RPA=3,2;RU=T;SEQQ=62;STR;STRANDQ=1;STRQ=93;TLOD=7.40	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:27,1:0.066:28:2,0:21,0:25,2,0,1	0/1:27,3:0.125:30:3,1:20,0:24,3,0,3
CONTQ=56;DP=63;ECNT=2;GERMQ=93;MBQ=25,14;MFRL=0,0;MMQ=95,73;MPOS=35;NALOD=1.52;NLOD=9.63;POPAF=6.00;SEQQ=30;STRANDQ=1;TLOD=4.15	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:32,0:0.029:32:4,0:28,0:28,4,0,0	0/1:29,2:0.091:31:3,0:25,0:25,4,0,2
CONTQ=87;DP=85;ECNT=2;GERMQ=93;MBQ=27,14;MFRL=0,0;MMQ=94,91;MPOS=39;NALOD=-2.717e-01;NLOD=11.66;POPAF=6.00;RPA=2,1;RU=C;SEQQ=65;STR;STRANDQ=1;STRQ=93;TLOD=7.76	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:50,1:0.038:51:41,0:8,0:9,41,1,0	0/1:30,4:0.139:34:27,0:1,1:3,27,4,0
CONTQ=55;DP=86;ECNT=2;GERMQ=93;MBQ=23,14;MFRL=0,0;MMQ=94,92;MPOS=53;NALOD=-2.626e+00;NLOD=7.90;PON;POPAF=6.00;RPA=2,1;RU=C;SEQQ=20;STR;STRANDQ=4;STRQ=93;TLOD=3.11	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:49,2:0.056:51:26,0:9,0:10,39,0,2	0/1:32,2:0.084:34:21,0:6,0:7,25,0,2
CONTQ=45;DP=96;ECNT=1;GERMQ=93;MBQ=26,28;MFRL=0,0;MMQ=76,92;MPOS=38;NALOD=1.74;NLOD=16.21;POPAF=4.31;SEQQ=24;STRANDQ=1;TLOD=4.09	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:54,0:0.018:54:50,0:1,0:3,51,0,0	0/1:38,3:0.093:41:33,0:1,3:3,35,3,0
CONTQ=70;DP=92;ECNT=1;GERMQ=93;MBQ=27,25;MFRL=0,0;MMQ=90,85;MPOS=31;NALOD=-4.304e+00;NLOD=4.91;PON;POPAF=6.00;RPA=1,2;RU=C;SEQQ=56;STR;STRANDQ=6;STRQ=93;TLOD=6.67	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:47,3:0.062:50:46,2:0,1:0,47,1,2	0/1:33,3:0.102:36:33,3:0,0:0,33,0,3
CONTQ=93;DP=259;ECNT=2;GERMQ=93;MBQ=22,20;MFRL=0,0;MMQ=84,77;MPOS=41;NALOD=-1.244e+01;NLOD=15.57;PON;POPAF=6.00;RPA=5,6;RU=G;SEQQ=93;STR;STRANDQ=41;STRQ=93;TLOD=16.50	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:141,10:0.070:151:87,5:9,0:30,111,3,7	0/1:94,12:0.117:106:61,6:9,1:26,68,2,10
CONTQ=60;DP=54;ECNT=2;GERMQ=93;MBQ=27,14;MFRL=0,0;MMQ=92,82;MPOS=34;NALOD=-1.550e+00;NLOD=3.93;PON;POPAF=6.00;SEQQ=27;STRANDQ=1;TLOD=3.88	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:30,2:0.084:32:12,0:18,0:18,12,0,2	0/1:20,2:0.125:22:5,0:15,0:15,5,0,2
CONTQ=74;DP=71;ECNT=1;GERMQ=93;MBQ=24,13;MFRL=0,0;MMQ=93,91;MPOS=5;NALOD=-4.033e+00;NLOD=2.34;PON;POPAF=6.00;SEQQ=52;STRANDQ=1;TLOD=6.50	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:39,4:0.101:43:19,0:14,1:16,23,4,0	0/1:22,3:0.148:25:12,0:4,0:5,17,3,0
CONTQ=54;DP=55;ECNT=2;GERMQ=93;MBQ=27,14;MFRL=0,0;MMQ=87,81;MPOS=59;NALOD=1.28;NLOD=5.42;POPAF=6.00;SEQQ=21;STRANDQ=4;TLOD=3.23	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:18,0:0.050:18:4,0:14,0:14,4,0,0	0/1:35,2:0.077:37:7,0:25,0:26,9,2,0
CONTQ=67;DP=70;ECNT=2;GERMQ=93;MBQ=20,15;MFRL=0,0;MMQ=89,94;MPOS=34;NALOD=-8.859e-01;NLOD=3.29;POPAF=6.00;RPA=2,1;RU=T;SEQQ=41;STR;STRANDQ=23;STRQ=93;TLOD=5.18	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:22,1:0.079:23:8,0:7,0:12,10,0,1	0/1:42,3:0.085:45:15,1:9,0:24,18,2,1
CONTQ=93;DP=135;ECNT=3;GERMQ=93;MBQ=25,23;MFRL=0,0;MMQ=94,90;MPOS=33;NALOD=-8.107e+00;NLOD=5.86;PON;POPAF=6.00;RPA=5,6;RU=G;SEQQ=85;STR;STRANDQ=57;STRQ=93;TLOD=9.70	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:75,6:0.084:81:57,4:15,1:15,60,2,4	0/1:47,6:0.127:53:30,2:14,3:14,33,3,3
CONTQ=78;DP=139;ECNT=3;GERMQ=93;MBQ=27,14;MFRL=0,0;MMQ=93,88;MPOS=46;NALOD=-1.145e+01;NLOD=3.30;POPAF=6.00;SEQQ=69;STRANDQ=1;TLOD=7.93	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:78,6:0.081:84:57,0:18,0:18,60,0,6	0/1:51,4:0.088:55:34,0:17,0:17,34,0,4
CONTQ=63;DP=143;ECNT=3;GERMQ=93;MBQ=27,17;MFRL=0,0;MMQ=93,83;MPOS=18;NALOD=-2.750e+00;NLOD=16.65;PON;POPAF=6.00;SEQQ=44;STRANDQ=3;TLOD=5.48	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:84,3:0.041:87:68,2:15,0:16,68,0,3	0/1:53,3:0.069:56:36,1:16,0:17,36,0,3
CONTQ=80;DP=129;ECNT=1;GERMQ=93;MBQ=25,20;MFRL=0,0;MMQ=94,91;MPOS=53;NALOD=-1.552e+00;NLOD=15.88;PON;POPAF=6.00;RPA=4,3;RU=G;SEQQ=47;STR;STRANDQ=31;STRQ=93;TLOD=5.71	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:74,2:0.038:76:63,2:4,0:8,66,0,2	0/1:47,4:0.093:51:42,1:1,0:3,44,1,3
CONTQ=91;DP=66;ECNT=1;GERMQ=93;MBQ=26,26;MFRL=0,0;MMQ=90,87;MPOS=22;NALOD=-3.224e+00;NLOD=4.84;PON;POPAF=6.00;RPA=2,1;RU=G;SEQQ=70;STR;STRANDQ=1;STRQ=93;TLOD=8.59	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:39,2:0.069:41:38,0:0,2:0,39,2,0	0/1:20,4:0.192:24:19,0:0,2:0,20,4,0
CONTQ=58;DP=65;ECNT=2;GERMQ=93;MBQ=26,10;MFRL=0,0;MMQ=96,83;MPOS=9;NALOD=-5.623e-01;NLOD=7.14;POPAF=6.00;RPA=2,1;RU=C;SEQQ=23;STR;STRANDQ=1;STRQ=93;TLOD=3.39	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:35,1:0.052:36:12,0:20,0:20,15,0,1	0/1:25,2:0.103:27:5,0:15,0:15,10,0,2
CONTQ=57;DP=73;ECNT=2;GERMQ=93;MBQ=24,16;MFRL=0,0;MMQ=95,91;MPOS=24;NALOD=-2.507e+00;NLOD=5.77;PON;POPAF=6.00;RPA=3,2;RU=C;SEQQ=19;STR;STRANDQ=1;STRQ=93;TLOD=3.02	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:41,2:0.066:43:14,1:19,0:20,21,0,2	0/1:27,2:0.097:29:3,1:15,0:16,11,0,2
CONTQ=52;DP=105;ECNT=2;GERMQ=93;MBQ=27,13;MFRL=0,0;MMQ=91,91;MPOS=58;NALOD=1.80;NLOD=18.66;POPAF=6.00;SEQQ=19;STRANDQ=1;TLOD=3.04	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:62,0:0.016:62:48,0:13,0:13,49,0,0	0/1:41,2:0.067:43:34,0:6,0:6,35,2,0
CONTQ=67;DP=105;ECNT=2;GERMQ=93;MBQ=27,13;MFRL=0,0;MMQ=91,87;MPOS=55;NALOD=-6.672e+00;NLOD=4.45;PON;POPAF=6.00;RPA=3,2;RU=C;SEQQ=38;STR;STRANDQ=1;STRQ=93;TLOD=4.91	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:58,4:0.078:62:48,0:9,2:9,49,4,0	0/1:40,3:0.089:43:35,0:4,1:5,35,3,0
CONTQ=52;DP=17;ECNT=3;GERMQ=77;MBQ=27,25;MFRL=0,0;MMQ=93,81;MPOS=24;NALOD=1.18;NLOD=4.21;POPAF=6.00;SEQQ=14;STRANDQ=7;TLOD=3.42	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|0:14,0:0.063:14:9,0:3,0:0|1:1119533_TC_T:1119533:5,9,0,0	0|1:2,1:0.400:3:1,0:1,1:0|1:1119533_TC_T:1119533:1,1,1,0
CONTQ=52;DP=17;ECNT=3;GERMQ=77;MBQ=25,24;MFRL=0,0;MMQ=93,81;MPOS=21;NALOD=1.18;NLOD=4.21;POPAF=6.00;SEQQ=14;STRANDQ=7;TLOD=3.42	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|0:14,0:0.063:14:9,0:1,0:0|1:1119533_TC_T:1119533:5,9,0,0	0|1:2,1:0.400:3:1,0:1,1:0|1:1119533_TC_T:1119533:1,1,1,0
CONTQ=52;DP=17;ECNT=3;GERMQ=77;MBQ=24,24;MFRL=0,0;MMQ=93,81;MPOS=16;NALOD=1.18;NLOD=4.21;POPAF=6.00;RPA=5,4;RU=G;SEQQ=14;STR;STRANDQ=7;STRQ=93;TLOD=3.42	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|0:14,0:0.063:14:8,0:5,0:0|1:1119533_TC_T:1119533:5,9,0,0	0|1:2,1:0.400:3:0,0:1,1:0|1:1119533_TC_T:1119533:1,1,1,0
CONTQ=57;DP=93;ECNT=1;GERMQ=93;MBQ=27,23;MFRL=0,0;MMQ=90,82;MPOS=9;NALOD=-5.165e+00;NLOD=7.97;PON;POPAF=6.00;RPA=2,1;RU=G;SEQQ=25;STR;STRANDQ=21;STRQ=93;TLOD=3.65	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:61,3:0.061:64:30,0:24,3:28,33,3,0	0/1:27,2:0.097:29:15,0:11,1:11,16,1,1
CONTQ=85;DP=96;ECNT=4;GERMQ=93;MBQ=26,14;MFRL=0,0;MMQ=93,82;MPOS=46;NALOD=-2.187e+00;NLOD=9.40;PON;POPAF=6.00;RPA=3,2;RU=C;SEQQ=66;STR;STRANDQ=1;STRQ=93;TLOD=7.75	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:53,3:0.052:56:34,0:14,1:19,34,2,1	0/1:34,4:0.125:38:18,0:13,2:15,19,4,0
CONTQ=56;DP=63;ECNT=4;GERMQ=93;MBQ=26,15;MFRL=0,0;MMQ=96,91;MPOS=50;NALOD=1.49;NLOD=9.03;PON;POPAF=6.00;RPA=2,1;RU=G;SEQQ=20;STR;STRANDQ=4;STRQ=93;TLOD=3.13	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:30,0:0.031:30:22,0:7,0:7,23,0,0	0/1:31,2:0.086:33:21,0:7,0:7,24,0,2
CONTQ=70;DP=71;ECNT=4;GERMQ=93;MBQ=24,12;MFRL=0,0;MMQ=96,90;MPOS=16;NALOD=-1.505e+00;NLOD=3.97;PON;POPAF=6.00;SEQQ=55;STRANDQ=3;TLOD=6.59	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:30,2:0.083:32:20,0:6,0:7,23,0,2	0/1:34,3:0.102:37:23,0:7,0:7,27,0,3
CONTQ=93;DP=108;ECNT=4;GERMQ=93;MBQ=27,14;MFRL=0,0;MMQ=94,85;MPOS=38;NALOD=-5.271e+00;NLOD=5.39;PON;POPAF=6.00;SEQQ=83;STRANDQ=3;TLOD=9.35	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:53,3:0.069:56:44,0:7,0:7,46,0,3	0/1:47,5:0.109:52:36,1:7,0:7,40,0,5
CONTQ=93;DP=32;ECNT=2;GERMQ=85;MBQ=26,21;MFRL=0,0;MMQ=92,84;MPOS=7;NALOD=1.22;NLOD=4.51;PON;POPAF=6.00;RPA=4,3;RU=G;SEQQ=39;STR;STRANDQ=1;STRQ=93;TLOD=6.02	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:15,0:0.058:15:0,0:15,0:15,0,0,0	0/1:12,4:0.259:16:0,2:11,0:12,0,0,4
CONTQ=62;DP=32;ECNT=2;GERMQ=93;MBQ=23,19;MFRL=0,0;MMQ=92,91;MPOS=28;NALOD=1.23;NLOD=4.82;PON;POPAF=6.00;RPA=2,1;RU=T;SEQQ=28;STR;STRANDQ=3;STRQ=93;TLOD=4.14	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:16,0:0.056:16:2,0:11,0:14,2,0,0	0/1:14,2:0.167:16:5,0:7,1:9,5,2,0
CONTQ=93;DP=30;ECNT=1;GERMQ=55;MBQ=23,22;MFRL=0,0;MMQ=94,78;MPOS=9;NALOD=-5.977e-01;NLOD=3.06;POPAF=6.00;RPA=5,4;RU=G;SEQQ=71;STR;STRANDQ=8;STRQ=93;TLOD=9.96	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:20,1:0.087:21:14,1:1,0:5,15,0,1	0/1:5,4:0.455:9:4,4:1,0:1,4,0,4
CONTQ=93;DP=181;ECNT=1;GERMQ=93;MBQ=24,25;MFRL=0,0;MMQ=90,85;MPOS=72;NALOD=-1.193e+01;NLOD=5.89;PON;POPAF=6.00;RPA=6,7;RU=T;SEQQ=93;STR;STRANDQ=40;STRQ=93;TLOD=26.77	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:99,9:0.089:108:70,9:9,0:28,71,0,9	0/1:58,14:0.203:72:37,12:9,0:19,39,2,12
CONTQ=67;DP=228;ECNT=2;GERMQ=93;MBQ=23,14;MFRL=0,0;MMQ=89,84;MPOS=22;NALOD=-1.287e+01;NLOD=12.41;PON;POPAF=6.00;RPA=2,1;RU=T;SEQQ=30;STR;STRANDQ=3;STRQ=93;TLOD=4.16	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:124,12:0.062:136:71,4:30,0:40,84,0,12	0/1:85,4:0.045:89:45,1:24,0:26,59,0,4
CONTQ=68;DP=100;ECNT=2;GERMQ=93;MBQ=24,14;MFRL=0,0;MMQ=89,87;MPOS=41;NALOD=-7.594e+00;NLOD=2.21;PON;POPAF=6.00;SEQQ=47;STRANDQ=1;TLOD=5.81	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:53,4:0.084:57:20,0:26,0:33,20,0,4	0/1:38,3:0.093:41:13,0:15,0:24,14,0,3
CONTQ=77;DP=47;ECNT=2;GERMQ=93;MBQ=24,16;MFRL=0,0;MMQ=91,90;MPOS=11;NALOD=1.38;NLOD=6.48;PON;POPAF=6.00;RPA=3,2;RU=C;SEQQ=24;STR;STRANDQ=1;STRQ=93;TLOD=3.90	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:22,0:0.040:22:13,0:3,0:8,14,0,0	0/1:17,3:0.177:20:14,0:1,0:2,15,3,0
CONTQ=62;DP=74;ECNT=2;GERMQ=85;MBQ=23,20;MFRL=0,0;MMQ=89,91;MPOS=81;NALOD=-5.410e-01;NLOD=2.72;POPAF=6.00;RPA=3,4;RU=C;SEQQ=19;STR;STRANDQ=5;STRQ=93;TLOD=3.25	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:19,1:0.080:20:13,1:4,0:5,14,0,1	0/1:14,2:0.158:16:14,2:0,0:0,14,0,2
CONTQ=93;DP=41;ECNT=1;GERMQ=76;MBQ=25,22;MFRL=0,0;MMQ=93,86;MPOS=23;NALOD=-5.651e-01;NLOD=2.68;PON;POPAF=6.00;RPA=6,5;RU=C;SEQQ=59;STR;STRANDQ=48;STRQ=93;TLOD=7.73	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:19,1:0.092:20:8,0:6,0:7,12,0,1	0/1:16,4:0.227:20:5,1:11,2:11,5,2,2
CONTQ=76;DP=56;ECNT=1;GERMQ=93;MBQ=27,22;MFRL=0,0;MMQ=92,83;MPOS=40;NALOD=-2.563e+00;NLOD=3.61;PON;POPAF=6.00;RPA=4,3;RU=G;SEQQ=42;STR;STRANDQ=1;STRQ=93;TLOD=5.60	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:33,2:0.081:35:12,2:20,0:21,12,0,2	0/1:18,3:0.174:21:6,1:12,0:12,6,0,3
CONTQ=63;DP=34;ECNT=1;GERMQ=82;MBQ=23,19;MFRL=0,0;MMQ=92,93;MPOS=95;NALOD=0.489;NLOD=2.64;POPAF=6.00;RPA=2,3;RU=C;SEQQ=24;STR;STRANDQ=2;STRQ=93;TLOD=3.78	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:14,1:0.106:15:7,0:7,0:7,7,0,1	0/1:13,2:0.176:15:5,1:5,0:6,7,0,2
CONTQ=73;DP=70;ECNT=1;GERMQ=93;MBQ=24,12;MFRL=0,0;MMQ=93,71;MPOS=24;NALOD=1.63;NLOD=12.34;POPAF=6.00;SEQQ=36;STRANDQ=6;TLOD=4.80	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:41,0:0.023:41:35,0:0,0:0,41,0,0	0/1:25,3:0.130:28:23,0:0,0:0,25,0,3
CONTQ=57;DP=76;ECNT=2;GERMQ=93;MBQ=27,22;MFRL=0,0;MMQ=93,82;MPOS=67;NALOD=-4.709e+00;NLOD=4.10;PON;POPAF=6.00;RPA=4,3;RU=C;SEQQ=20;STR;STRANDQ=3;STRQ=93;TLOD=3.13	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:45,3:0.080:48:32,3:13,0:13,32,0,3	0/1:26,2:0.100:28:18,2:7,0:7,19,0,2
CONTQ=93;DP=80;ECNT=2;GERMQ=93;MBQ=27,21;MFRL=0,0;MMQ=93,83;MPOS=30;NALOD=0.121;NLOD=11.48;PON;POPAF=6.00;RPA=5,4;RU=G;SEQQ=93;STR;STRANDQ=56;STRQ=93;TLOD=21.85	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:48,1:0.039:49:34,0:13,0:13,35,0,1	0/1:22,9:0.304:31:16,6:6,2:6,16,2,7
CONTQ=61;DP=41;ECNT=2;GERMQ=93;MBQ=23,22;MFRL=0,0;MMQ=79,74;MPOS=54;NALOD=1.36;NLOD=6.62;POPAF=6.00;RPA=4,3;RU=C;SEQQ=21;STR;STRANDQ=6;STRQ=93;TLOD=3.41	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:22,0:0.042:22:20,0:2,0:2,20,0,0	0/1:16,2:0.149:18:11,2:0,0:0,16,0,2
CONTQ=93;DP=48;ECNT=2;GERMQ=66;MBQ=23,12;MFRL=0,0;MMQ=78,58;MPOS=3;NALOD=-1.055e+00;NLOD=3.12;PON;POPAF=6.00;SEQQ=37;STRANDQ=6;TLOD=6.55	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:22,1:0.079:23:18,0:1,0:2,20,0,1	0/1:18,6:0.266:24:16,1:0,0:0,18,0,6
CONTQ=77;DP=50;ECNT=1;GERMQ=93;MBQ=28,14;MFRL=0,0;MMQ=94,91;MPOS=15;NALOD=1.51;NLOD=9.33;POPAF=6.00;RPA=1,2;RU=C;SEQQ=37;STR;STRANDQ=1;STRQ=93;TLOD=5.21	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:31,0:0.030:31:3,0:26,0:26,5,0,0	0/1:16,3:0.190:19:3,0:11,0:11,5,0,3
CONTQ=65;DP=37;ECNT=1;GERMQ=90;MBQ=26,22;MFRL=0,0;MMQ=94,88;MPOS=74;NALOD=-3.568e-01;NLOD=4.44;PON;POPAF=6.00;RPA=6,5;RU=G;SEQQ=19;STR;STRANDQ=2;STRQ=93;TLOD=3.56	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:25,1:0.072:26:5,1:19,0:20,5,0,1	0/1:9,2:0.232:11:3,1:6,0:6,3,0,2
CONTQ=63;DP=32;ECNT=3;GERMQ=93;MBQ=27,23;MFRL=0,0;MMQ=95,91;MPOS=6;NALOD=1.28;NLOD=5.40;POPAF=6.00;RPA=1,2;RU=G;SEQQ=27;STR;STRANDQ=2;STRQ=93;TLOD=4.17	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:18,0:0.050:18:13,0:3,0:3,15,0,0	0/1:12,2:0.187:14:3,2:7,0:7,5,0,2
CONTQ=60;DP=57;ECNT=3;GERMQ=93;MBQ=27,19;MFRL=0,0;MMQ=92,94;MPOS=52;NALOD=-9.357e-01;NLOD=6.50;PON;POPAF=6.00;SEQQ=30;STRANDQ=1;TLOD=4.19	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:34,1:0.054:35:31,0:3,0:3,31,1,0	0/1:19,2:0.130:21:14,0:5,1:5,14,2,0
CONTQ=93;DP=115;ECNT=3;GERMQ=93;MBQ=26,13;MFRL=0,0;MMQ=94,94;MPOS=12;NALOD=-7.106e-02;NLOD=15.86;PON;POPAF=6.00;RPA=2,1;RU=A;SEQQ=93;STR;STRANDQ=1;STRQ=93;TLOD=13.39	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:64,1:0.030:65:48,0:13,0:15,49,1,0	0/1:43,6:0.137:49:22,0:16,1:20,23,6,0
CONTQ=80;DP=120;ECNT=1;GERMQ=93;MBQ=24,13;MFRL=0,0;MMQ=96,91;MPOS=18;NALOD=-4.433e+00;NLOD=10.05;PON;POPAF=6.00;RPA=2,1;RU=A;SEQQ=56;STR;STRANDQ=1;STRQ=93;TLOD=6.69	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:67,3:0.055:70:42,0:18,0:24,43,3,0	0/1:46,4:0.096:50:16,0:12,0:29,17,4,0
CONTQ=59;DP=62;ECNT=2;GERMQ=93;MBQ=26,19;MFRL=0,0;MMQ=97,93;MPOS=16;NALOD=1.58;NLOD=11.14;POPAF=6.00;SEQQ=24;STRANDQ=1;TLOD=3.54	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:37,0:0.025:37:11,0:21,0:21,16,0,0	0/1:22,2:0.115:24:2,0:17,0:17,5,0,2
CONTQ=88;DP=74;ECNT=2;GERMQ=93;MBQ=21,20;MFRL=0,0;MMQ=97,92;MPOS=19;NALOD=-7.383e-02;NLOD=9.02;PON;POPAF=6.00;RPA=3,4;RU=C;SEQQ=59;STR;STRANDQ=1;STRQ=93;TLOD=7.25	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:41,2:0.047:43:20,1:10,0:21,20,0,2	0/1:27,4:0.151:31:8,2:8,0:17,10,0,4
CONTQ=92;DP=78;ECNT=1;GERMQ=93;MBQ=25,20;MFRL=0,0;MMQ=95,90;MPOS=26;NALOD=-4.640e+00;NLOD=4.67;PON;POPAF=6.00;RPA=3,2;RU=C;SEQQ=73;STR;STRANDQ=1;STRQ=93;TLOD=8.88	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:48,3:0.075:51:22,2:23,0:24,24,0,3	0/1:19,4:0.199:23:7,2:9,0:9,10,0,4
CONTQ=54;DP=103;ECNT=1;GERMQ=93;MBQ=27,15;MFRL=0,0;MMQ=94,90;MPOS=87;NALOD=-4.167e-01;NLOD=15.51;POPAF=6.00;RPA=2,1;RU=C;SEQQ=22;STR;STRANDQ=2;STRQ=93;TLOD=3.29	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:63,1:0.030:64:28,1:16,0:21,42,0,1	0/1:35,2:0.077:37:12,0:5,0:14,21,0,2
CONTQ=69;DP=88;ECNT=1;GERMQ=93;MBQ=26,20;MFRL=0,0;MMQ=97,80;MPOS=35;NALOD=-1.641e+00;NLOD=8.61;POPAF=6.00;RPA=4,5;RU=A;SEQQ=30;STR;STRANDQ=2;STRQ=93;TLOD=4.13	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:48,2:0.057:50:29,2:14,0:18,30,0,2	0/1:35,3:0.100:38:22,3:8,0:13,22,0,3
CONTQ=56;DP=60;ECNT=1;GERMQ=93;MBQ=25,14;MFRL=0,0;MMQ=92,90;MPOS=47;NALOD=-8.237e-01;NLOD=4.43;POPAF=6.00;RPA=2,1;RU=G;SEQQ=21;STR;STRANDQ=1;STRQ=93;TLOD=3.19	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:26,1:0.069:27:11,0:11,0:11,15,0,1	0/1:31,2:0.086:33:9,1:13,0:16,15,0,2
CONTQ=93;DP=102;ECNT=2;GERMQ=93;MBQ=25,20;MFRL=0,0;MMQ=91,91;MPOS=67;NALOD=-3.070e+00;NLOD=6.03;PON;POPAF=6.00;RPA=3,2;RU=C;SEQQ=93;STR;STRANDQ=1;STRQ=93;TLOD=14.37	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:47,3:0.074:50:41,1:0,0:0,47,1,2	0/1:43,6:0.137:49:38,0:0,4:2,41,6,0
CONTQ=50;DP=98;ECNT=2;GERMQ=93;MBQ=26,22;MFRL=0,0;MMQ=91,90;MPOS=62;NALOD=1.41;NLOD=14.75;PON;POPAF=6.00;RPA=2,1;RU=G;SEQQ=19;STR;STRANDQ=1;STRQ=93;TLOD=3.04	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:49,0:0.019:49:47,0:0,0:0,49,0,0	0/1:46,2:0.060:48:39,0:2,2:5,41,2,0
CONTQ=66;DP=105;ECNT=1;GERMQ=93;MBQ=23,20;MFRL=0,0;MMQ=84,75;MPOS=23;NALOD=-6.663e+00;NLOD=2.39;PON;POPAF=6.00;RPA=4,5;RU=G;SEQQ=27;STR;STRANDQ=7;STRQ=93;TLOD=3.82	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:53,5:0.099:58:49,5:1,0:2,51,0,5	0/1:43,3:0.083:46:42,3:1,0:1,42,0,3
CONTQ=66;DP=19;ECNT=3;GERMQ=68;MBQ=25,12;MFRL=0,0;MMQ=91,86;MPOS=15;NALOD=1.04;NLOD=3.01;PON;POPAF=6.00;SEQQ=33;STRANDQ=5;TLOD=5.21	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:10,0:0.083:10:6,0:4,0:4,6,0,0	0/1:6,2:0.298:8:2,0:3,0:4,2,2,0
CONTQ=66;DP=18;ECNT=3;GERMQ=65;MBQ=22,14;MFRL=0,0;MMQ=91,90;MPOS=37;NALOD=1.02;NLOD=2.71;POPAF=6.00;RPA=1,2;RU=G;SEQQ=29;STR;STRANDQ=3;STRQ=93;TLOD=4.81	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:9,0:0.088:9:5,0:1,0:1,8,0,0	0/1:6,2:0.300:8:3,0:2,0:2,4,2,0
CONTQ=65;DP=25;ECNT=3;GERMQ=88;MBQ=25,25;MFRL=0,0;MMQ=89,88;MPOS=19;NALOD=1.18;NLOD=4.21;POPAF=6.00;SEQQ=41;STRANDQ=1;TLOD=5.73	GT:AD:AF:DP:F1R2:F2R1:SB	0/0:14,0:0.063:14:10,0:1,0:1,13,0,0	0/1:9,2:0.231:11:7,0:0,2:1,8,2,0

@davidbenjamin
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@sahilseth It should be fixed now, but what stack trace are you getting?

@sahilseth
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java.lang.IllegalArgumentException: errorRateLog10 must be good probability but got NaN
        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:730)
        at org.broadinstitute.hellbender.utils.QualityUtils.phredScaleLog10ErrorRate(QualityUtils.java:321)
        at org.broadinstitute.hellbender.utils.QualityUtils.phredScaleErrorRate(QualityUtils.java:307)
        at org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter.PreAdapterOrientationScorer.scoreOrientationBiasMetricsOverContext(PreAdapterOrientationScorer.java:78)
        at org.broadinstitute.hellbender.tools.exome.FilterByOrientationBias.onTraversalStart(FilterByOrientationBias.java:191)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:964)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
        at org.broadinstitute.hellbender.Main.main(Main.java:291)

These calls are from IonTorrent platform (not Illumina), maybe that could be an issue?

@sahilseth
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sahilseth commented Apr 22, 2019 •
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I think this could because this is single end sequencing. I had run the previous step of collecting metrics with defaults. It seems all of them are rightfully geared towards PE, and all reads are thrown out in my case.

I am now re-running the previous step, as follows - welcome suggestions - thanks

4.1.1.0/gatk CollectSequencingArtifactMetrics \
 -I T_nochr.bam \
 -O T -R hg19_nochr.fasta \
 --INCLUDE_NON_PF_READS true --INCLUDE_UNPAIRED true \
 --MAXIMUM_INSERT_SIZE 0 --MINIMUM_INSERT_SIZE 0

@davidbenjamin
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@sahilseth This is actually a different issue. The solution is to not run CollectSequencingArtifactMetrics and any other tools involved in orientation bias filtering. Single-end reads do not have orientation bias artifacts and the whole model assumes paired reads.

For the record, we recently deprecated CollectSequencingArtifactMetrics and FilterByOrientationBias in favor of our new orientation bias workflow that uses LearnReadOrientationModel. But for single-end sequencing you shouldn't use the old workflow or the new workflow.

@amizeranschi amizeranschi mentioned this issue May 22, 2019
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fix edge case for Mutect2 germline resource broadinstitute/gatk
5 participants
@sahilseth @byoo @davidbenjamin @bounlu @MikeWLloyd