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Fixed an edge case in HaplotypeCaller where filtered alleles in the v…
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…icinity of forced-calling alleles could result in empty calls (#7740)
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@jamesemery
jamesemery authored Mar 30, 2022
1 parent a85c25f commit 527e5d7
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Showing 3 changed files with 122 additions and 5 deletions.
10 changes: 5 additions & 5 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,8 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
}

final AFCalculationResult AFresult = alleleFrequencyCalculator.calculate(reducedVC, defaultPloidy);
final OutputAlleleSubset outputAlternativeAlleles = calculateOutputAlleleSubset(AFresult, vc, givenAlleles);
final Set<Allele> forcedAlleles = AssemblyBasedCallerUtils.getAllelesConsistentWithGivenAlleles(givenAlleles, vc);
final OutputAlleleSubset outputAlternativeAlleles = calculateOutputAlleleSubset(AFresult, vc, forcedAlleles);

// note the math.abs is necessary because -10 * 0.0 => -0.0 which isn't nice
final double log10Confidence =
Expand All @@ -162,7 +163,7 @@ public VariantContext calculateGenotypes(final VariantContext vc, final Genotype
// return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
// skip this if we are already looking at a vc with NON_REF as the first alt allele i.e. if we are in GenotypeGVCFs
if ( !passesEmitThreshold(phredScaledConfidence, outputAlternativeAlleles.siteIsMonomorphic) && !emitAllActiveSites()
&& noAllelesOrFirstAlleleIsNotNonRef(outputAlternativeAlleles.alleles) && givenAlleles.isEmpty()) {
&& noAllelesOrFirstAlleleIsNotNonRef(outputAlternativeAlleles.alleles) && forcedAlleles.isEmpty()) {
return null;
}

Expand Down Expand Up @@ -290,18 +291,17 @@ public List<Integer> alternativeAlleleMLECounts() {
* Provided the exact mode computations it returns the appropriate subset of alleles that progress to genotyping.
* @param afCalculationResult the allele fraction calculation result.
* @param vc the variant context
* @param forcedAlleles alleles from the vc input that are consistent with forced alleles in the assembly region {@link AssemblyBasedCallerUtils#getAllelesConsistentWithGivenAlleles}
* @return information about the alternative allele subsetting {@code null}.
*/
private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult afCalculationResult, final VariantContext vc, final List<VariantContext> givenAlleles) {
private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalculationResult afCalculationResult, final VariantContext vc, final Set<Allele> forcedAlleles) {
final List<Allele> outputAlleles = new ArrayList<>();
final List<Integer> mleCounts = new ArrayList<>();
boolean siteIsMonomorphic = true;
final List<Allele> alleles = afCalculationResult.getAllelesUsedInGenotyping();
final int alternativeAlleleCount = alleles.size() - 1;
int referenceAlleleSize = 0;

final Set<Allele> forcedAlleles = AssemblyBasedCallerUtils.getAllelesConsistentWithGivenAlleles(givenAlleles, vc);

for (final Allele allele : alleles) {
if (allele.isReference() ) {
referenceAlleleSize = allele.length();
Expand Down
34 changes: 34 additions & 0 deletions ...oadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -672,6 +672,40 @@ public void testForceCalling(final String bamPath, final File forceCallingVcf, f
}
}

@Test
public void testForceCallingNotProducingNoCalls() throws IOException {
Utils.resetRandomGenerator();
final String bamPath = NA12878_20_21_WGS_bam;
final File forceCallingVcf = new File(TEST_FILES_DIR, "testGenotypeGivenAllelesMode_givenAlleles.vcf");
final String intervalString = "20:10000000-10010000";
final File expected = new File(TEST_FILES_DIR, "expected.testForceCallingNotProducingNoCalls.gatk4.vcf");


final File output = createTempFile("testGenotypeGivenAllelesMode", ".vcf");
final String outputPath = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected.getAbsolutePath() : output.getAbsolutePath();

// Prior to https://github.com/broadinstitute/gatk/pull/7740 the output for this test would be littered with 0/0 reference variants with empty alt alleles. This test is intended to enshrine the new behavior.
// For an example of what the output used to look at see the issue https://github.com/broadinstitute/gatk/issues/7741.
final String[] args = {
"-I", bamPath,
"-R", b37Reference,
"-L", intervalString,
"-O", outputPath,
"-pairHMM", "AVX_LOGLESS_CACHING",
"--" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, "false",
"--" + AssemblyBasedCallerArgumentCollection.FORCE_CALL_ALLELES_LONG_NAME, forceCallingVcf.getAbsolutePath(),
"--" + AssemblyBasedCallerArgumentCollection.ALLELE_EXTENSION_LONG_NAME, "2",
"--" + GenotypeCalculationArgumentCollection.CALL_CONFIDENCE_LONG_NAME, "1000" // This is intended to be an absurdly high number that forces most alleles to fail to demonstrate a bug that caused calls to be made in the vicinity of forced alleles
};

runCommandLine(args);

if ( ! UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
IntegrationTestSpec.assertEqualTextFiles(output, expected);
}
}


// regression test for https://github.com/broadinstitute/gatk/issues/6495, where a mistake in assembly region trimming
// caused variants in one-base or similarly short intervals to cause reads to be trimmed to one base long, yielding
// no calls.
Expand Down
83 changes: 83 additions & 0 deletions ...e/hellbender/tools/haplotypecaller/expected.testForceCallingNotProducingNoCalls.gatk4.vcf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,83 @@
##fileformat=VCFv4.2
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
20 10000439 . T G 2819.06 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.86;QD=25.36;SOR=1.236 GT:AD:DP:GQ:PL 1/1:0,80:80:99:2833,240,0
20 10000598 . T A 1956.06 . AC=2;AF=1.00;AN=2;DP=51;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.45;QD=28.73;SOR=1.225 GT:AD:DP:GQ:PL 1/1:0,49:49:99:1970,147,0
20 10000694 . G A 1029.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.599;DP=87;ExcessHet=0.0000;FS=1.822;MLEAC=1;MLEAF=0.500;MQ=48.86;MQRankSum=-5.114;QD=12.56;ReadPosRankSum=0.657;SOR=0.566 GT:AD:DP:GQ:PL 0/1:45,37:82:99:1037,0,1601
20 10000758 . T A 3853.06 . AC=2;AF=1.00;AN=2;DP=97;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.51;QD=30.97;SOR=0.802 GT:AD:DP:GQ:PL 1/1:0,95:95:99:3867,286,0
20 10001298 . T A 2932.06 . AC=2;AF=1.00;AN=2;DP=79;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=53.93;QD=27.24;SOR=0.963 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2946,220,0
20 10001436 . A AAGGCT 2325.03 . AC=2;AF=1.00;AN=2;DP=58;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=41.22;QD=28.20;SOR=3.014 GT:AD:DP:GQ:PL 1/1:0,52:52:99:2339,156,0
20 10001474 . C T 2655.06 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=44.87;QD=25.00;SOR=1.516 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2669,219,0
20 10001617 . C A 1752.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.261;DP=105;ExcessHet=0.0000;FS=13.163;MLEAC=1;MLEAF=0.500;MQ=59.02;MQRankSum=1.373;QD=17.02;ReadPosRankSum=-0.280;SOR=1.346 GT:AD:DP:GQ:PL 0/1:52,51:103:99:1760,0,1781
20 10001628 . G A 3913.06 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.19;QD=29.56;SOR=1.053 GT:AD:DP:GQ:PL 1/1:0,95:95:99:3927,285,0
20 10001661 . T C 3621.06 . AC=2;AF=1.00;AN=2;DP=85;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.13;QD=30.62;SOR=1.112 GT:AD:DP:GQ:PL 1/1:0,83:83:99:3635,249,0
20 10001670 . T G 3688.06 . AC=2;AF=1.00;AN=2;DP=86;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.60;QD=28.17;SOR=0.897 GT:AD:DP:GQ:PL 1/1:0,84:84:99:3702,253,0
20 10002058 . T G 2978.06 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.931;DP=79;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=57.87;MQRankSum=3.068;QD=26.80;ReadPosRankSum=0.624;SOR=0.776 GT:AD:DP:GQ:PL 1/1:1,74:75:99:2992,216,0
20 10002099 . C T 1215.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=68;ExcessHet=0.0000;FS=3.528;MLEAC=1;MLEAF=0.500;MQ=56.46;MQRankSum=-0.850;QD=18.70;ReadPosRankSum=0.173;SOR=0.375 GT:AD:DP:GQ:PL 0/1:27,38:65:99:1223,0,844
20 10002138 . C G 2458.06 . AC=2;AF=1.00;AN=2;DP=57;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.64;QD=26.00;SOR=0.765 GT:AD:DP:GQ:PL 1/1:0,56:56:99:2472,169,0
20 10002142 . G C 2422.06 . AC=2;AF=1.00;AN=2;DP=56;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.08;QD=30.02;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2436,166,0
20 10002470 . C T 2537.06 . AC=2;AF=1.00;AN=2;DP=68;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.92;QD=31.98;SOR=0.859 GT:AD:DP:GQ:PL 1/1:0,63:63:99:2551,189,0
20 10002625 . G T 2680.06 . AC=2;AF=1.00;AN=2;DP=66;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.08;QD=27.51;SOR=1.127 GT:AD:DP:GQ:PL 1/1:0,64:64:99:2694,193,0
20 10003021 . C T 2398.06 . AC=2;AF=1.00;AN=2;DP=63;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.04;QD=29.11;SOR=1.071 GT:AD:DP:GQ:PL 1/1:0,60:60:99:2412,181,0
20 10003358 . A C 1475.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.004;DP=91;ExcessHet=0.0000;FS=0.844;MLEAC=1;MLEAF=0.500;MQ=59.80;MQRankSum=1.011;QD=16.58;ReadPosRankSum=-1.355;SOR=0.572 GT:AD:DP:GQ:PL 0/1:45,44:89:99:1483,0,1477
20 10003651 . T C 3635.06 . AC=2;AF=1.00;AN=2;DP=98;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.24;QD=28.08;SOR=1.511 GT:AD:DP:GQ:PL 1/1:0,93:93:99:3649,279,0
20 10003692 . A G 2624.06 . AC=2;AF=1.00;AN=2;DP=72;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.48;QD=23.23;SOR=1.352 GT:AD:DP:GQ:PL 1/1:0,68:68:99:2638,205,0
20 10003832 . G A 2720.06 . AC=2;AF=1.00;AN=2;DP=67;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.82;QD=29.03;SOR=1.473 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2734,199,0
20 10004094 . A C,T 1840.06 . AC=2,0;AF=1.00,0.00;AN=2;DP=55;ExcessHet=0.0000;FS=0.000;MLEAC=2,0;MLEAF=1.00,0.00;MQ=52.62;QD=34.72;SOR=1.524 GT:AD:DP:GQ:PL 1/1:0,53,0:53:99:1854,157,0,1899,164,2091
20 10004147 . A G 1852.06 . AC=2;AF=1.00;AN=2;DP=54;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.19;QD=30.67;SOR=1.136 GT:AD:DP:GQ:PL 1/1:0,52:52:99:1866,156,0
20 10004351 . C G 2770.06 . AC=2;AF=1.00;AN=2;DP=71;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.05;QD=26.61;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2784,211,0
20 10004389 . T G 2509.06 . AC=2;AF=1.00;AN=2;DP=67;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.62;QD=29.20;SOR=1.143 GT:AD:DP:GQ:PL 1/1:0,62:62:99:2523,187,0
20 10004610 . A C 3640.06 . AC=2;AF=1.00;AN=2;DP=93;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.75;QD=28.55;SOR=0.761 GT:AD:DP:GQ:PL 1/1:0,89:89:99:3654,267,0
20 10004769 . TAAAACTATGC T 1011.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=80;ExcessHet=0.0000;FS=3.758;MLEAC=1;MLEAF=0.500;MQ=52.80;MQRankSum=-6.625;QD=15.81;ReadPosRankSum=1.879;SOR=1.306 GT:AD:DP:GQ:PL 0/1:37,27:64:99:1019,0,1471
20 10004771 . A *,T 0 LowQual AC=1,0;AF=0.500,0.00;AN=2;DP=75;ExcessHet=0.0000;FS=2.397;MLEAC=1,0;MLEAF=0.500,0.00;MQ=52.28;MQRankSum=-6.325;QD=-0.00;ReadPosRankSum=2.117;SOR=1.115 GT:AD:DP:GQ:PL 0/1:32,27,0:59:99:1028,0,1345,1163,1304,2853
20 10004874 . A C 3617.06 . AC=2;AF=1.00;AN=2;DP=90;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.35;QD=34.42;SOR=1.286 GT:AD:DP:GQ:PL 1/1:0,87:87:99:3631,261,0
20 10004887 . A G 1344.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=90;ExcessHet=0.0000;FS=1.793;MLEAC=1;MLEAF=0.500;MQ=59.49;MQRankSum=-0.067;QD=15.82;ReadPosRankSum=-1.114;SOR=0.984 GT:AD:DP:GQ:PL 0/1:45,40:85:99:1352,0,1542
20 10005010 . C T 2949.06 . AC=2;AF=1.00;AN=2;DP=73;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.68;QD=28.53;SOR=1.226 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2963,217,0
20 10005427 . C T 2229.06 . AC=2;AF=1.00;AN=2;DP=60;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=27.23;SOR=0.729 GT:AD:DP:GQ:PL 1/1:0,55:55:99:2243,165,0
20 10005499 . A G 3068.06 . AC=2;AF=1.00;AN=2;DP=78;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.52;SOR=1.121 GT:AD:DP:GQ:PL 1/1:0,76:76:99:3082,229,0
20 10005587 . A G 1250.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.834;DP=76;ExcessHet=0.0000;FS=1.955;MLEAC=1;MLEAF=0.500;MQ=59.75;MQRankSum=-0.972;QD=17.37;ReadPosRankSum=0.248;SOR=0.848 GT:AD:DP:GQ:PL 0/1:36,36:72:99:1258,0,1236
20 10005723 . A G 3077.06 . AC=2;AF=1.00;AN=2;DP=88;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.79;QD=33.47;SOR=0.947 GT:AD:DP:GQ:PL 1/1:0,86:86:99:3091,258,0
20 10006404 . A C 2943.06 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.22;QD=32.91;SOR=1.432 GT:AD:DP:GQ:PL 1/1:0,76:76:99:2957,228,0
20 10006682 . T A 2889.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.44;QD=31.31;SOR=1.179 GT:AD:DP:GQ:PL 1/1:0,73:73:99:2903,219,0
20 10006819 . AAAAC A 2554.03 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.06;QD=31.45;SOR=0.762 GT:AD:DP:GQ:PL 1/1:0,58:58:99:2568,176,0
20 10006823 . C *,G 0 LowQual AC=2,0;AF=1.00,0.00;AN=2;DP=76;ExcessHet=0.0000;FS=0.000;MLEAC=2,0;MLEAF=1.00,0.00;MQ=61.13;QD=-0.00;SOR=0.762 GT:AD:DP:GQ:PL 1/1:0,58,0:58:99:2567,175,0,2618,220,3157
20 10007175 . C T 1371.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.249;DP=63;ExcessHet=0.0000;FS=2.211;MLEAC=1;MLEAF=0.500;MQ=59.63;MQRankSum=1.319;QD=22.49;ReadPosRankSum=-1.213;SOR=0.434 GT:AD:DP:GQ:PL 0/1:23,38:61:99:1379,0,780
20 10007352 . C T 2779.06 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.67;QD=33.27;SOR=1.054 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2793,208,0
20 10007531 . A G 2935.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.75;QD=31.26;SOR=1.577 GT:AD:DP:GQ:PL 1/1:0,72:72:99:2949,217,0
20 10007980 . A C 3539.06 . AC=2;AF=1.00;AN=2;DP=92;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.70;QD=27.76;SOR=0.990 GT:AD:DP:GQ:PL 1/1:0,90:90:99:3553,270,0
20 10008029 . T TA 2010.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.409;DP=97;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=61.11;MQRankSum=0.651;QD=26.10;ReadPosRankSum=-1.357;SOR=0.774 GT:AD:DP:GQ:PL 1/1:3,74:77:99:2024,145,0
20 10008146 . TA T 2165.03 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.56;QD=30.93;SOR=0.874 GT:AD:DP:GQ:PL 1/1:0,70:70:99:2179,211,0
20 10008221 . T C 3239.06 . AC=2;AF=1.00;AN=2;DP=83;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.17;QD=29.09;SOR=0.850 GT:AD:DP:GQ:PL 1/1:0,80:80:99:3253,240,0
20 10008458 . T G 2669.06 . AC=2;AF=1.00;AN=2;DP=72;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=52.76;QD=26.08;SOR=0.980 GT:AD:DP:GQ:PL 1/1:0,69:69:99:2683,207,0
20 10008738 . C CGTTT,CGTTTGTTT Infinity . AC=0,0;AF=0.00,0.00;AN=2;DP=49;ExcessHet=0.0000;FS=0.000;MLEAC=0,0;MLEAF=0.00,0.00;MQ=37.97;SOR=0.389 GT:AD:DP:GQ:PL 0/0:47,0,0:47:99:0,142,2074,142,2074,2074
20 10008948 . TA T 2091.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=56;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.26;MQRankSum=1.946;QD=33.85;ReadPosRankSum=0.884;SOR=0.721 GT:AD:DP:GQ:PL 1/1:1,53:54:99:2105,117,0
20 10009227 . A G 1390.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220;DP=63;ExcessHet=0.0000;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=56.82;MQRankSum=1.428;QD=22.43;ReadPosRankSum=-1.159;SOR=0.281 GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740
20 10009246 . A G 3017.06 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=55.68;QD=27.08;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0
20 10009400 . T A 3013.06 . AC=2;AF=1.00;AN=2;DP=75;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.42;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0
20 10009512 . C G 3054.06 . AC=2;AF=1.00;AN=2;DP=80;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.53;QD=27.65;SOR=1.223 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3068,231,0
20 10009719 . A G 1901.06 . AC=2;AF=1.00;AN=2;DP=65;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.71;QD=33.35;SOR=1.047 GT:AD:DP:GQ:PL 1/1:0,57:57:99:1915,170,0
20 10009795 . A G 1895.06 . AC=2;AF=1.00;AN=2;DP=49;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.62;QD=29.48;SOR=1.514 GT:AD:DP:GQ:PL 1/1:0,47:47:99:1909,141,0
20 10009879 . A G 2259.06 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.534;DP=53;ExcessHet=0.0000;FS=8.605;MLEAC=2;MLEAF=1.00;MQ=50.48;MQRankSum=1.681;QD=30.56;ReadPosRankSum=1.113;SOR=1.198 GT:AD:DP:GQ:PL 1/1:2,51:53:99:2273,150,0
20 10009883 . A G 2166.06 . AC=2;AF=1.00;AN=2;DP=52;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=50.81;QD=33.63;SOR=1.755 GT:AD:DP:GQ:PL 1/1:0,49:49:99:2180,147,0

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