From a85c25fc607f6440b6b7e43c05d92ace196bc216 Mon Sep 17 00:00:00 2001
From: ldgauthier <gauthier@broadinstitute.org>
Date: Wed, 30 Mar 2022 10:59:57 -0400
Subject: [PATCH] Fix for NPE when GDB has too many alleles (#7738)

* Fix for NPE when GDB has too many alleles and many GQ0 hom-ref genotypes
allow variant to pass QUAL filter
---
 .../genotyper/AlleleSubsettingUtils.java      |    7 +
 .../walkers/genotyper/GenotypingEngine.java   |   11 +-
 .../afcalc/AlleleFrequencyCalculator.java     |   10 +-
 .../hellbender/utils/GenotypeUtils.java       |    7 +-
 .../walkers/GenotypeGVCFsIntegrationTest.java |   17 +
 .../GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf | 3432 +++++++++++++++++
 .../test.tooManyAltsNoPLs.g.vcf.idx           |  Bin 0 -> 114082 bytes
 7 files changed, 3477 insertions(+), 7 deletions(-)
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf
 create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf.idx

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java
index ed272a3e3bd..660bf634393 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/AlleleSubsettingUtils.java
@@ -295,6 +295,9 @@ public static List<Allele> calculateMostLikelyAlleles(final VariantContext vc, f
         Utils.nonNull(vc, "vc is null");
         Utils.validateArg(defaultPloidy > 0, () -> "default ploidy must be > 0 but defaultPloidy=" + defaultPloidy);
         Utils.validateArg(numAltAllelesToKeep > 0, () -> "numAltAllelesToKeep must be > 0, but numAltAllelesToKeep=" + numAltAllelesToKeep);
+        //allow PLs or GPs (as for GATK-DRAGEN), but we need some kind of genotype data
+        Utils.validateArg(vc.getGenotypes().stream().anyMatch(g -> g.hasPL() || g.hasExtendedAttribute(VCFConstants.GENOTYPE_POSTERIORS_KEY)), () -> "Most likely alleles cannot be calculated without likelihoods");
+        //NOTE: this is used in the reblocking case when we have a hom-ref GT and real ALTs
         final boolean allHomRefData = vc.getGenotypes().stream().allMatch(g -> g.hasPL() && g.getPL()[0] == 0);  //PL=[0,0,0] is okay, we just don't want confident variants
 
         final boolean hasSymbolicNonRef = vc.hasAllele(Allele.NON_REF_ALLELE);
@@ -306,6 +309,10 @@ public static List<Allele> calculateMostLikelyAlleles(final VariantContext vc, f
         }
 
         final double[] likelihoodSums = calculateLikelihoodSums(vc, defaultPloidy, allHomRefData);
+        if (MathUtils.sum(likelihoodSums) == 0.0 && !allHomRefData) {
+            throw new IllegalStateException("No likelihood sum exceeded zero -- method was called for variant data " +
+                    "with no variant information.");
+        }
         return filterToMaxNumberOfAltAllelesBasedOnScores(numAltAllelesToKeep, vc.getAlleles(), likelihoodSums);
     }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
index e346db6cc83..d8094bf9149 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypingEngine.java
@@ -112,10 +112,13 @@ public Config getConfiguration() {
     }
 
     /**
-     * Main entry function to calculate genotypes of a given VC with corresponding GLs that is shared across genotypers (namely GGVCFs and HC).
+     * Main entry function to calculate genotypes of a given VC with corresponding GLs that is shared across
+     * genotypers (namely GGVCFs and HC).
      *
      * Completes a variant context with genotype calls and associated annotations given the genotype likelihoods and
-     * the model that need to be applied.
+     * the model that need to be applied.  Hom-ref likelihoods can be approximated from GQs, but if no genotype has
+     * likelihoods then that variant is either all-ref or contains variants with no likelihoods, and in both cases
+     * we want to exit.
      *
      * @param vc                                 Input variant context to complete.
      * @return                                   VC with assigned genotypes
@@ -393,7 +396,7 @@ boolean isVcCoveredByDeletion(final VariantContext vc) {
      */
     protected final boolean cannotBeGenotyped(final VariantContext vc) {
         if (vc.getNAlleles() <= GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED
-                && vc.getGenotypes().stream().anyMatch(GenotypeUtils::genotypeIsUsableForAFCalculation)) {
+            && vc.getGenotypes().stream().anyMatch(Genotype::hasLikelihoods)) {  //likelihoods may be missing when reading from GenomicsDB if there are more alts that GDB args allow
             return false;
         }
         // protect against too many alternate alleles that we can't even run AF on:
@@ -402,7 +405,7 @@ protected final boolean cannotBeGenotyped(final VariantContext vc) {
                     " alleles. Site will be skipped at location " + vc.getContig() + ":" + vc.getStart());
             return true;
         }else {
-            logger.warn("No genotype contained sufficient data to recalculate genotypes. Site will be skipped at location "
+            logger.warn("No genotype contained sufficient data to recalculate site and allele qualities. Site will be skipped at location "
                     + vc.getContig() + ":" + vc.getStart());
             return true;
         }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java
index df71708e600..8943594d57f 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java
@@ -124,14 +124,20 @@ public AFCalculationResult calculate(final VariantContext vc) {
      * Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
      *
      * @param vc the VariantContext holding the alleles and sample information.  The VariantContext
-     *           must have at least 1 alternative allele
+     *           must have at least 1 alternative allele and at least one variant genotype with likelihoods.
+     *           Hom-ref genotype likelihoods can be approximated, but the result will be zero allele counts without
+     *           likelihoods for a non-reference genotype.
      * @return result (for programming convenience)
      */
     public AFCalculationResult calculate(final VariantContext vc, final int defaultPloidy) {
         Utils.nonNull(vc, "VariantContext cannot be null");
+        Utils.validate(vc.getGenotypes().stream().anyMatch(Genotype::hasLikelihoods),
+                "VariantContext  at " + vc.getContig() + ":" + vc.getStart() + "must contain at least one " +
+                        "genotype with likelihoods -- did this VC exceed the max number of alt alleles?");
         final int numAlleles = vc.getNAlleles();
         final List<Allele> alleles = vc.getAlleles();
-        Utils.validateArg( numAlleles > 1, () -> "VariantContext has only a single reference allele, but getLog10PNonRef requires at least one at all " + vc);
+        Utils.validateArg( numAlleles > 1, () -> "VariantContext  at " + vc.getContig() + ":" + vc.getStart() +
+                "has only a single reference allele, but getLog10PNonRef requires at least alternate allele");
 
         final double[] priorPseudocounts = alleles.stream()
                 .mapToDouble(a -> a.isReference() ? refPseudocount : (a.length() == vc.getReference().length() ? snpPseudocount : indelPseudocount)).toArray();
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java
index 3dccec42b16..77e920a918c 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java
@@ -82,7 +82,12 @@ public static GenotypeCounts computeDiploidGenotypeCounts(final VariantContext v
             }
 
             // Genotype::getLikelihoods returns a new array, so modification in-place is safe
-            final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10ToLinearSpace(g.getLikelihoods().getAsVector());
+            final double[] normalizedLikelihoods;
+            if (g.hasLikelihoods()) {
+                normalizedLikelihoods = MathUtils.normalizeFromLog10ToLinearSpace(g.getLikelihoods().getAsVector());
+            } else {
+                throw new IllegalStateException("Genotype has no likelihoods: " + g.toString());
+            }
             final double[] biallelicLikelihoods;
 
             //if there are multiple alts, use the biallelic PLs for the best alt
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
index 8e73d650328..c52e2c7aab5 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
@@ -345,6 +345,23 @@ public void testGDBMaxAltsEqualsGGVCFsMaxAlts() {
         File output = runGenotypeGVCFS(genomicsDBUri, null, args, b37_reference_20_21);
     }
 
+    @Test
+    public void testGenotypingOnVCWithMissingPLs() {
+        //this regression test input:
+        // 1) is missing PLs because it had more than the allowed number of alts for GDB
+        // 2) has enough GQ0 samples to achieve a QUAL high enough to pass the initial threshold
+        final String input = toolsTestDir + "/walkers/GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf";
+        final List<String> args = new ArrayList<String>();
+        args.add("-G");
+        args.add("StandardAnnotation");
+        args.add("-G");
+        args.add("AS_StandardAnnotation");
+        final File output = runGenotypeGVCFS(input, null, args, hg38Reference);
+        final Pair<VCFHeader, List<VariantContext>> outputData = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath());
+        //only variant is a big variant that shouldn't get output because it is missing PLs, but we should skip it gracefully
+        Assert.assertEquals(outputData.getRight().size(), 0);
+    }
+
     private void runAndCheckGenomicsDBOutput(final ArgumentsBuilder args, final File expected, final File output) {
         Utils.resetRandomGenerator();
         runCommandLine(args);
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf
new file mode 100644
index 00000000000..85e9c0b5821
--- /dev/null
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/test.tooManyAltsNoPLs.g.vcf
@@ -0,0 +1,3432 @@
+##fileformat=VCFv4.2
+##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=PASS,Description="All filters passed">
+##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=GP,Number=G,Type=Float,Description="genotype posterior in Phred Scale">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
+##FORMAT=<ID=PG,Number=G,Type=Float,Description="genotype priors in Phred Scale">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
+##GATKCommandLine=<ID=GenomicsDBImport,CommandLine="GenomicsDBImport --genomicsdb-workspace-path genomicsdb --batch-size 50 --consolidate true --sample-name-map /cromwell_root/fc-7f30aedd-ee43-47cf-9ba0-4ec848dd230a/027d57bd-78db-4d77-8ecf-6907eb06fb13/GenerateSampleMap/e4746657-77aa-4d5d-a426-4b6b60bfd964/call-GenerateSampleMapFile/all-dragen.sample_map --merge-input-intervals true --reader-threads 5 --intervals /cromwell_root/fc-7f30aedd-ee43-47cf-9ba0-4ec848dd230a/8f17f343-e1fb-4fae-96b1-c856e31d860e/JointGenotyping/fc0cc4a1-63ec-4b05-8c0a-121950827559/call-SplitIntervalList/cacheCopy/glob-d928cd0f5fb17b6bd5e635f48c18ccfb/3179-scattered.interval_list --gcs-project-for-requester-pays broad-dsde-methods --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --validate-sample-name-map false --max-num-intervals-to-import-in-parallel 1 --merge-contigs-into-num-partitions 0 --genomicsdb-shared-posixfs-optimizations false --bypass-feature-reader false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 0 --cloud-index-prefetch-buffer 0 --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 --disable-tool-default-read-filters false",Version="4.2.5.0",Date="February 18, 2022 9:01:14 PM GMT">
+##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output test.tooManyAltsNoPLs.g.vcf --genomicsdb-max-alternate-alleles 10 --call-genotypes true --variant gendb://genomicsdb --intervals chr8:12560676 --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --genomicsdb-use-bcf-codec false --genomicsdb-shared-posixfs-optimizations false --genomicsdb-use-gcs-hdfs-connector false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.2.5.0-19-ge43dbac-SNAPSHOT",Date="March 21, 2022 3:54:35 PM EDT">
+##GVCFBlock0-10=minGQ=0(inclusive),maxGQ=10(exclusive)
+##GVCFBlock10-20=minGQ=10(inclusive),maxGQ=20(exclusive)
+##GVCFBlock20-30=minGQ=20(inclusive),maxGQ=30(exclusive)
+##GVCFBlock30-40=minGQ=30(inclusive),maxGQ=40(exclusive)
+##GVCFBlock40-50=minGQ=40(inclusive),maxGQ=50(exclusive)
+##GVCFBlock50-60=minGQ=50(inclusive),maxGQ=60(exclusive)
+##GVCFBlock60-100=minGQ=60(inclusive),maxGQ=100(exclusive)
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AS_BaseQRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities">
+##INFO=<ID=AS_FS,Number=A,Type=Float,Description="allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele">
+##INFO=<ID=AS_InbreedingCoeff,Number=A,Type=Float,Description="Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=AS_MQ,Number=A,Type=Float,Description="Allele-specific RMS Mapping Quality">
+##INFO=<ID=AS_MQRankSum,Number=A,Type=Float,Description="Allele-specific Mapping Quality Rank Sum">
+##INFO=<ID=AS_QD,Number=A,Type=Float,Description="Allele-specific Variant Confidence/Quality by Depth">
+##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
+##INFO=<ID=AS_RAW_BaseQRankSum,Number=1,Type=String,Description="raw data for allele specific rank sum test of base qualities">
+##INFO=<ID=AS_RAW_MQ,Number=1,Type=String,Description="Allele-specfic raw data for RMS Mapping Quality">
+##INFO=<ID=AS_RAW_MQRankSum,Number=1,Type=String,Description="Allele-specfic raw data for Mapping Quality Rank Sum">
+##INFO=<ID=AS_RAW_ReadPosRankSum,Number=1,Type=String,Description="allele specific raw data for rank sum test of read position bias">
+##INFO=<ID=AS_ReadPosRankSum,Number=A,Type=Float,Description="allele specific Z-score from Wilcoxon rank sum test of each Alt vs. Ref read position bias">
+##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
+##INFO=<ID=AS_SOR,Number=A,Type=Float,Description="Allele specific strand Odds Ratio of 2x|Alts| contingency table to detect allele specific strand bias">
+##INFO=<ID=AS_VarDP,Number=1,Type=String,Description="Allele-specific (informative) depth over variant genotypes -- including ref, RAW format">
+##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=DRAGstrInfo,Number=2,Type=Integer,Description="Indicates the period and repeat count">
+##INFO=<ID=DRAGstrParams,Number=3,Type=Float,Description="Parameters used (GOP, GCP, API)">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=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=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=MQ_DP,Number=1,Type=Integer,Description="Depth over variant samples for better MQ calculation (deprecated -- use RAW_MQandDP instead.)">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
+##INFO=<ID=RAW_GT_COUNT,Number=3,Type=Integer,Description="Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity">
+##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=VarDP,Number=1,Type=Integer,Description="(informative) depth over variant genotypes">
+##contig=<ID=chr1,length=248956422,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr2,length=242193529,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr3,length=198295559,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr4,length=190214555,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr5,length=181538259,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr6,length=170805979,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr7,length=159345973,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr8,length=145138636,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr9,length=138394717,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr10,length=133797422,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr11,length=135086622,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr12,length=133275309,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr13,length=114364328,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr14,length=107043718,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr15,length=101991189,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr16,length=90338345,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr17,length=83257441,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr18,length=80373285,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr19,length=58617616,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr20,length=64444167,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr21,length=46709983,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chr22,length=50818468,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chrX,length=156040895,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chrY,length=57227415,assembly=Homo_sapiens_assembly38.fasta.gz>
+##contig=<ID=chrM,length=16569,assembly=Homo_sapiens_assembly38.fasta.gz>
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9117	SRS179118	SRS179120	SRS179121	SRS179123	SRS179124	SRS179126	SRS179127	SRS179129	SRS179130	SRS179132	SRS179133	SRS179184	SRS179185	SRS179187	SRS179188	SRS179190	SRS179191	SRS179193	SRS179194	SRS179196	SRS179197	SRS179199	SRS179200	SRS179202	SRS179203	SRS179205	SRS179206	SRS179208	SRS179209	SRS184283	SRS184284	SRS184286	SRS184287	SRS184289	SRS184290	SRS184292	SRS184293	SRS184295	SRS184296	SRS184298	SRS184299	SRS184302	SRS184304	SRS184305	SRS184307	SRS184308	SRS184310	SRS184311	SRS184315	SRS184316	SRS184318	SRS184319	SRS191033	SRS191034	SRS191036	SRS191037	SRS191039	SRS191040	SRS191042	SRS191043	SRS191045	SRS191046	SRS191048	SRS191049	SRS191051	SRS191052	SRS191054	SRS191055	SRS191057	SRS191058	SRS191060	SRS191063	SRS191064	SRS191066	SRS191067	SRS191069	SRS191070	SRS191072	SRS191073	SRS191075	SRS191076	SRS191078	SRS191079	SRS191081	SRS191082	SRS191084	SRS191085	SRS191087	SRS191088	SRS191090	SRS191091	SRS191093	SRS191094	SRS193276	SRS193277	SRS212451	SRS212452	SRS212454	SRS212455	SRS212458	SRS212459	SRS212468	SRS212469	SRS212471	SRS212472	SRS212495	SRS212496	SRS212515	SRS212516	SRS212521	SRS212522	SRS212524	SRS212525	SRS212527	SRS212528	SRS212530	SRS212531	SRS290867	SRS290868	SRS290870	SRS290871	SRS290873	SRS290874	SRS290876	SRS290877	SRS290879	SRS290880	SRS290882	SRS290883	SRS290885	SRS290886	SRS290888	SRS290889	SRS290891	SRS290892	SRS290894	SRS290895	SRS290897	SRS290898	SRS290900	SRS290901	SRS290903	SRS290904	SRS290906	SRS290907	SRS290909	SRS290910	SRS290912	SRS290913	SRS290915	SRS290916	SRS290918	SRS290919	SRS290921	SRS290922	SRS290924	SRS290925	SRS290927	SRS290928	SRS290930	SRS290931	SRS290933	SRS290934	SRS290936	SRS290937	SRS290939	SRS290940	SRS290942	SRS290943	SRS290945	SRS290946	SRS290948	SRS290949	SRS290951	SRS290952	SRS290954	SRS290955	SRS343971	SRS343972	SRS343974	SRS343975	SRS343977	SRS343978	SRS343980	SRS343981	SRS343983	SRS343984	SRS343986	SRS343987	SRS343989	SRS343990	SRS343992	SRS343993	SRS343995	SRS343996	SRS343998	SRS343999	SRS344001	SRS344002	SRS344004	SRS344005	SRS344007	SRS344008	SRS344010	SRS344011	SRS344013	SRS344014	SRS344016	SRS344017	SRS344019	SRS344020	SRS344022	SRS344023	SRS344025	SRS344026	SRS344031	SRS344032	SRS344034	SRS344035	SRS344037	SRS344038	SRS344040	SRS344041	SRS344043	SRS344044	SRS344052	SRS344053	SRS344056	SRS344057	SRS344062	SRS344063	SRS344065	SRS344066	SRS344068	SRS344069	SRS344071	SRS344072	SRS344074	SRS344075	SRS344077	SRS344078	SRS344080	SRS344081	SRS344083	SRS344084	SRS344086	SRS344087	SRS344089	SRS344090	SRS344092	SRS344093	SRS344095	SRS344096	SRS344098	SRS344099	SRS344101	SRS344102	SRS344104	SRS344105	SRS350638	SRS350639	SRS350641	SRS350642	SRS350644	SRS350645	SRS350647	SRS350648	SRS350650	SRS350651	SRS350653	SRS350654	SRS350658	SRS350666	SRS350683	SRS350684	SRS350701	SRS350702	SRS350710	SRS350719	SRS350721	SRS350722	SRS350724	SRS350727	SRS350728	SRS350730	SRS350731	SRS350733	SRS350734	SRS350742	SRS350743	SRS350745	SRS350746	SRS350748	SRS350749	SRS350751	SRS350752	SRS350754	SRS350755	SRS350757	SRS350758	SRS350760	SRS350761	SRS350763	SRS350764	SRS350766	SRS350767	SRS350769	SRS350770	SRS350772	SRS350773	SRS350775	SRS350776	SRS350781	SRS350782	SRS350784	SRS350785	SRS350787	SRS350788	SRS350790	SRS350791	SRS350796	SRS350797	SRS350800	SRS350802	SRS350803	SRS350806	SRS350809	SRS350811	SRS350812	SRS350814	SRS350815	SRS350817	SRS350818	SRS350820	SRS350821	SRS350823	SRS350824	SRS350826	SRS350827	SRS350829	SRS350831	SRS350833	SRS350835	SRS350836	SRS350838	SRS350839	SRS350840	SRS350841	SRS350845	SRS350846	SRS350847	SRS350848	SRS350850	SRS350851	SRS350853	SRS350854	SRS350855	SRS350856	SRS350860	SRS350861	SRS350865	SRS350867	SRS350868	SRS350890	SRS350893	SRS350900	SRS350903	SRS351003	SRS351004	SRS352794	SRS352795	SRS352806	SRS352809	SRS352811	SRS352812	SRS352814	SRS352815	SRS352817	SRS352818	SRS352827	SRS352832	SRS352840	SRS352844	SRS352846	SRS352853	SRS352855	SRS352905	SRS368094	SRS368096	SRS368097	SRS368100	SRS368103	SRS368105	SRS368106	SRS368108	SRS368109	SRS368111	SRS368112	SRS368115	SRS368120	SRS368121	SRS368168	SRS368170	SRS368175	SRS368176	SRS368178	SRS368179	SRS368193	SRS368194	SRS368205	SRS368206	SRS368208	SRS368209	SRS368213	SRS368215	SRS368220	SRS368221	SRS368227	SRS368236	SRS368237	SRS368239	SRS368240	SRS368244	SRS368245	SRS368247	SRS368248	SRS368250	SRS368251	SRS368253	SRS368254	SRS368256	SRS368257	SRS368259	SRS368260	SRS368262	SRS368263	SRS368265	SRS368266	SRS368268	SRS368269	SRS368271	SRS368272	SRS368274	SRS368275	SRS368278	SRS368280	SRS368283	SRS368284	SRS368286	SRS368287	SRS368290	SRS368332	SRS368334	SRS368338	SRS368341	SRS368344	SRS368345	SRS368347	SRS368350	SRS368351	SRS368397	SRS368402	SRS368404	SRS368405	SRS368469	SRS368470
+chr8	12560676	.	GTGTA	*,GTATATATATACACGTATATATACACGTATACATGTA,ATGTA,GTATATATATACACGTATATATATACACGTATATATGTA,GTATATATATACACGTATATATACACGTATATATGTA,GTATATATGTACACGTATATATATACACGTATATATGTATATATGTACACGTATATATATACACGTATATATGTATATATATACACGTATATATGTA,GTATATATGTACACGTATATATATACACGTATATATGTATATATATACACGTATATATACACGTATATATGTA,G,GTATATATATACACGTATATATATACACGTATATATGTATATATATACACGTATATATATACACGTATATATGTTTATATATACACGTATATATACACGTATATATGTA,GTATATATGTA,GTATATATATACACGTATATATACACGTATATATGTATATATATACACGTATATATATACACGTATATATGTA,GTATATATATACACGTATATATACACGTATATATGTATATATACACGTATATATACACGTATATATGTATATATACACACGTATATATACACGTATATATGTATATATACACACGTATATATACACGTATATATGTATATATATACACGTATATATACACGTATATATGTATATATATACACGTATATATACACGTATATATGTA,GTATATATATACACGTATATATATACACGTATATATATACACGTATATATACACGTATATATGTA,<NON_REF>	.	.	AS_QUALapprox=|0|76|173|3694|540|118|11|289|860|756|983|525|80|0;AS_RAW_BaseQRankSum=|0.000,1,0.400,1,0.600,1|-0.800,1,0.000,3,0.400,1|-0.900,1,0.000,3,0.600,1|-1.300,1,-0.900,1,-0.300,1,0.000,2,0.400,1,0.600,1|-2.000,1,-0.200,1,0.000,3,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1|0.000,4,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1|-0.700,1,0.000,3,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1|0.000,3,0.400,1,0.600,1;AS_RAW_MQ=603210.000|828996.000|23409.000|58122.000|352091.000|109421.000|16045.000|324.000|40669.000|7200.000|22096.000|0.000|15159.000|15887.000|18667.000;AS_RAW_MQRankSum=|-2.900,1,-2.800,1,-2.200,1,-1.900,1,-1.800,1,-1.600,1,-1.200,1,-0.100,1,2.400,1|-2.900,1,-2.800,1,-2.200,1,-2.000,1,-1.900,1|-4.600,1,-2.900,1,-2.800,2,-2.000,1,1.600,1|-3.100,1,-3.000,1,-2.800,2,-2.100,1,-2.000,2,-1.900,1,0.000,1|-2.900,1,-2.800,1,-2.600,1,-2.200,1,-2.000,2,-1.900,1,-0.800,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1,0.200,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1|-3.600,1,-2.900,1,-2.800,2,-2.600,1,-2.000,1,-1.900,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1|-2.900,1,-2.800,2,-1.900,1,-1.100,1|-2.900,1,-2.800,2,-2.000,1,-1.900,1;AS_RAW_ReadPosRankSum=|-2.500,1,-0.300,1,-0.200,1,0.100,1,0.400,1,1.200,1,1.900,1,2.500,1,3.000,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.400,1|-2.500,1,-2.400,1,-0.200,1,0.000,1,1.400,1,2.500,1|-3.300,1,-2.500,1,-1.200,1,-0.600,1,-0.200,1,0.000,2,0.400,1,2.500,1|-2.500,1,-0.100,1,0.000,1,0.200,1,0.400,1,1.800,1,2.500,1,2.600,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.500,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.500,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.100,1,2.500,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.500,1|-2.600,1,-2.500,1,-0.200,1,0.000,1,0.400,1,1.100,1,2.500,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.500,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.500,1|-2.500,1,-0.300,1,-0.200,1,0.400,1,2.500,1|-2.500,1,-0.200,1,0.000,1,0.400,1,2.500,1;AS_SB_TABLE=104,97|196,158|7,5|16,11|88,88|28,41|3,2|0,1|9,5|2,0|8,4|0,0|13,5|6,8|16,13;AS_VarDP=217|354|32|27|194|87|5|1|14|2|12|0|18|14|0;BaseQRankSum=-0.465;DP=215998;MQRankSum=-2.225;QUALapprox=8589;RAW_GT_COUNT=0,9,20;RAW_MQandDP=4517986,2097;ReadPosRankSum=0.334;VarDP=977	GT:AD:GQ:PGT:PID:PS:SB:DP	0/1:29,17,0,0,0,0,0,0,0,0,0,0,0,0,0:34:.:.:.:19,10,13,8:46	0/0:.:0:.:.:.:.:107	0/0:.:0:.:.:.:.:86	0/0:.:0:.:.:.:.:119	0/0:.:0:.:.:.:.:58	0/0:.:0:.:.:.:.:131	0/0:.:0:.:.:.:.:136	1/1:5,43,0,0,0,0,0,0,0,0,0,0,0,0,0:26:.:.:.:1,4,25,19:48	0/0:.:0:.:.:.:.:94	0/0:.:0:.:.:.:.:90	0/0:.:0:.:.:.:.:105	0/0:.:0:.:.:.:.:98	0/0:.:0:.:.:.:.:129	0/0:.:0:.:.:.:.:116	0/0:.:0:.:.:.:.:37	0/0:.:0:.:.:.:.:125	0/0:.:0:.:.:.:.:106	0/0:.:0:.:.:.:.:117	0/0:.:0:.:.:.:.:104	0/1:47,48,0,0,0,0,0,0,0,0,0,0,0,0,0:38:.:.:.:23,24,25,25:95	0/0:.:0:.:.:.:.:82	0/0:.:0:.:.:.:.:119	0/0:.:0:.:.:.:.:86	0/0:.:0:.:.:.:.:79	0/0:.:0:.:.:.:.:124	0/0:.:0:.:.:.:.:71	0/0:.:0:.:.:.:.:150	0/0:.:0:.:.:.:.:108	0/0:.:0:.:.:.:.:139	0/0:.:0:.:.:.:.:131	0/0:.:0:.:.:.:.:82	0/0:.:0:.:.:.:.:76	0/0:.:0:.:.:.:.:86	0/0:.:0:.:.:.:.:117	0/0:.:0:.:.:.:.:128	0|1:18,40,0,0,0,0,0,0,0,0,0,0,0,0,0:28:0|1:12560656_G_GTA:12560656:8,10,21,25:58	0/0:.:0:.:.:.:.:76	0/0:.:0:.:.:.:.:166	0/0:.:0:.:.:.:.:160	0/0:.:0:.:.:.:.:102	0/0:.:0:.:.:.:.:113	0/0:.:0:.:.:.:.:115	0/0:.:0:.:.:.:.:79	0/0:.:0:.:.:.:.:107	0/1:31,13,0,0,0,0,0,0,0,0,0,0,0,0,0:31:.:.:.:15,16,7,8:44	0/0:.:0:.:.:.:.:59	0/0:.:0:.:.:.:.:31	0/0:.:0:.:.:.:.:86	0/0:.:0:.:.:.:.:95	0|1:27,55,0,0,0,0,0,0,0,0,0,0,0,0,0:24:0|1:12560656_G_GTA:12560656:15,12,34,24:82	0/0:.:0:.:.:.:.:124	0/0:.:0:.:.:.:.:162	0/0:.:0:.:.:.:.:166	0/0:.:0:.:.:.:.:73	0/0:.:0:.:.:.:.:111	0/0:.:0:.:.:.:.:106	1/1:10,45,0,0,0,0,0,0,0,0,0,0,0,0,0:8:.:.:.:4,6,24,24:55	0/0:.:0:.:.:.:.:89	1/1:0,31,0,0,0,0,0,0,0,0,0,0,0,0,0:99:.:.:.:0,0,20,14:31	0/0:.:0:.:.:.:.:90	0/0:.:0:.:.:.:.:144	0/0:.:0:.:.:.:.:94	0/0:.:0:.:.:.:.:95	0/0:.:0:.:.:.:.:97	0/0:.:0:.:.:.:.:58	0/0:.:0:.:.:.:.:97	0/0:.:0:.:.:.:.:74	0/0:.:0:.:.:.:.:116	0/0:.:0:.:.:.:.:199	0/0:.:0:.:.:.:.:114	0/0:.:0:.:.:.:.:118	0/0:.:0:.:.:.:.:129	0/0:.:0:.:.:.:.:105	0/0:.:0:.:.:.:.:111	0/0:.:0:.:.:.:.:97	0/0:.:0:.:.:.:.:60	0/0:.:0:.:.:.:.:142	0/0:.:0:.:.:.:.:193	0/0:.:0:.:.:.:.:109	0/0:.:0:.:.:.:.:115	0/0:.:0:.:.:.:.:73	0/0:.:0:.:.:.:.:88	0/0:.:0:.:.:.:.:99	0/0:.:0:.:.:.:.:147	0/0:.:0:.:.:.:.:78	0/0:.:0:.:.:.:.:133	0/0:.:0:.:.:.:.:98	0/0:.:0:.:.:.:.:72	0/0:.:0:.:.:.:.:64	0/0:.:0:.:.:.:.:84	0/0:.:0:.:.:.:.:55	0/0:.:0:.:.:.:.:128	0/0:.:0:.:.:.:.:89	0/0:.:0:.:.:.:.:93	0/0:.:0:.:.:.:.:106	0/0:.:0:.:.:.:.:66	0/0:.:0:.:.:.:.:71	0/0:.:0:.:.:.:.:67	0/1:17,8,0,0,0,0,0,0,0,0,0,0,0,0,0:38:.:.:.:13,4,6,3:25	0/0:.:0:.:.:.:.:115	0/0:.:0:.:.:.:.:139	0/0:.:0:.:.:.:.:126	0/0:.:0:.:.:.:.:104	0/0:.:0:.:.:.:.:59	0/0:.:0:.:.:.:.:111	0/0:.:0:.:.:.:.:64	0/0:.:0:.:.:.:.:87	0/0:.:0:.:.:.:.:44	0/0:.:0:.:.:.:.:126	0/0:.:0:.:.:.:.:88	0/0:.:0:.:.:.:.:74	0/0:.:0:.:.:.:.:131	0/0:.:0:.:.:.:.:91	0/0:.:0:.:.:.:.:109	0/0:.:0:.:.:.:.:59	0/0:.:0:.:.:.:.:169	0/0:.:0:.:.:.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