From 3a5600377f3742f6805d953836a247adef20f5ca Mon Sep 17 00:00:00 2001
From: Karthik Gururaj <karthik.gururaj@intel.com>
Date: Thu, 8 Nov 2018 12:05:32 -0800
Subject: [PATCH] The newest release of GenomicsDB treats spanning deletions
 (spanning from earlier positions) as deletions in the min PL value
 computation. This behavior now matches the behavior of CombineGVCFs.

A more detailed description of the issue is provided in
https://github.com/broadinstitute/gatk/pull/4963

* Deleted a couple of files which are no longer necessary.
* Fixed the index of newMQcalc.combined.g.vcf
---
 build.gradle                                  |     2 +-
 .../GenomicsDBImportIntegrationTest.java      |     3 +-
 ...testGenomicsDBImportWithNonDiploidData.vcf |   640 +-
 ...GenomicsDBImportWithNonDiploidData.vcf.idx |   Bin 40774 -> 42427 bytes
 .../CombineGVCFs/newMQcalc.combined.g.vcf.idx |   Bin 844 -> 838 bytes
 .../GenomicsDBImport/newMQcalc.combined.g.vcf | 11613 ----------------
 .../newMQcalc.combined.g.vcf.idx              |   Bin 42528 -> 0 bytes
 7 files changed, 364 insertions(+), 11894 deletions(-)
 delete mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf
 delete mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf.idx

diff --git a/build.gradle b/build.gradle
index 111fdedef07..3ae10facd65 100644
--- a/build.gradle
+++ b/build.gradle
@@ -64,7 +64,7 @@ final sparkVersion = System.getProperty('spark.version', '2.2.0')
 final hadoopVersion = System.getProperty('hadoop.version', '2.8.2')
 final hadoopBamVersion = System.getProperty('hadoopBam.version','7.10.0')
 final tensorflowVersion = System.getProperty('tensorflow.version','1.9.0')
-final genomicsdbVersion = System.getProperty('genomicsdb.version','0.10.0-proto-3.0.0-beta-1+bdce8be25b873')
+final genomicsdbVersion = System.getProperty('genomicsdb.version','0.10.2-proto-3.0.0-beta-1+90dad1af8ce0e4d')
 final testNGVersion = '6.11'
 // Using the shaded version to avoid conflicts between its protobuf dependency
 // and that of Hadoop/Spark (either the one we reference explicitly, or the one
diff --git a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
index 83df10b5328..9a173e15597 100644
--- a/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
+++ b/src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java
@@ -57,6 +57,7 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
     private static final String NA_12878_PHASED = largeFileTestDir + "NA12878.phasedData.Chr20.vcf"; //NOTE: this is not phased according to the vcf spec but it reflects phasing currently produced by haplotype caller
     private static final String MULTIPLOID_DATA_HG37 = largeFileTestDir + "gvcfs/HapMap5plex.ploidy10.b37.g.vcf";
     private static final String NA12878_HG37 = toolsTestDir + "haplotypecaller/expected.testGVCFMode.gatk4.g.vcf";
+    //This file was generated by running CombineGVCFs on the input files
     private static final String MULTIPLOID_EXPECTED_RESULT = toolsTestDir + "GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf";
     private static final String MNP_GVCF = toolsTestDir + "GenomicsDBImport/mnp.input.g.vcf";
     private static final String ARTIFICIAL_PHASED = getTestDataDir() + "/ArtificalPhasedData.1.g.vcf";
@@ -116,7 +117,7 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
     private static final String ANOTHER_ATTRIBUTE_KEY = "AA";
 
     private static final List<String> GVCFS_WITH_NEW_MQ = Arrays.asList(toolsTestDir + "/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf", getTestDataDir() + "/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf");
-    private static final String COMBINED_WITH_NEW_MQ = toolsTestDir + "/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf";
+    private static final String COMBINED_WITH_NEW_MQ = toolsTestDir + "/walkers/CombineGVCFs/newMQcalc.combined.g.vcf";
     private static final List<SimpleInterval> INTERVAL2 = Arrays.asList(new SimpleInterval("20", 1, 11_000_000));
     private static final List<String> ATTRIBUTES_TO_IGNORE = Arrays.asList("RAW_MQ","RAW_MQandDP");  //CombineGVCFs doesn't support the old RAW_MQ anymore
 
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf
index 9f2edcf2d5c..c52e251cc1e 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf
@@ -1,7 +1,6 @@
 ##fileformat=VCFv4.2
 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
 ##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=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -11,8 +10,7 @@
 ##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=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 /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsdb-tests-5227961671712956466/workspace --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --variant /Users/gauthier/workspaces/gatk/src/test/resources/large/gvcfs/HapMap5plex.ploidy10.b37.g.vcf --batch-size 0 --reader-threads 1 --intervals 20:10000000-10100000 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --max-num-intervals-to-import-in-parallel 1 --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 --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 --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=Unavailable,Date="September 10, 2018 11:19:33 AM EDT">
-##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants  --output GDBdump.vcf --variant gendb:///var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsdb-tests-5227961671712956466/workspace --intervals 20:10000000-10100000 --reference src/test/resources/large/human_g1k_v37.20.21.fasta  --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 --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 --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 --disable-tool-default-read-filters false",Version=4.0.8.1-19-g2310a5f-SNAPSHOT,Date="September 10, 2018 11:21:17 AM EDT">
+##GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs  --output gold.g.vcf --variant ./src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --variant /home/karthikg/broad/gatk/src/test/resources/large/gvcfs/HapMap5plex.ploidy10.b37.g.vcf --reference src/test/resources/large/human_g1k_v37.20.21.fasta  --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --ignore-variants-starting-outside-interval 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 --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 --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.11.0-17-g2b48dcf-SNAPSHOT,Date="November 8, 2018 11:50:29 AM PST">
 ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
 ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
 ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
@@ -87,37 +85,121 @@
 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
 ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
 ##INFO=<ID=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=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
+##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">
-##contig=<ID=20,length=63025520,assembly=human_g1k_v37.20.21.fasta>
-##contig=<ID=21,length=48129895,assembly=human_g1k_v37.20.21.fasta>
-##reference=file:///Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenomicsDBImport
-##source=SelectVariants
+##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>
+##contig=<ID=3,length=198022430>
+##contig=<ID=4,length=191154276>
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+##contig=<ID=GL000213.1,length=164239>
+##contig=<ID=GL000211.1,length=166566>
+##contig=<ID=GL000199.1,length=169874>
+##contig=<ID=GL000217.1,length=172149>
+##contig=<ID=GL000216.1,length=172294>
+##contig=<ID=GL000215.1,length=172545>
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+##contig=<ID=GL000192.1,length=547496>
+##contig=<ID=NC_007605,length=171823>
+##source=CombineGVCFs
+##source=HaplotypeCaller
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	SAMPLE1
 20	10000000	.	T	<NON_REF>	.	.	END=10000116	GT:DP:GQ:MIN_DP:PL	./.:84:99:64:0,120,1800	./.
-20	10000117	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.14;DP=64;ExcessHet=3.01;MQRankSum=0.913;RAW_MQ=228169.00;ReadPosRankSum=-2.230e-01	GT:AD:DP:GQ:PL:SB	./.:36,28,0:64:99:934,0,1248,1042,1332,2374:16,20,19,9	./.
+20	10000117	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.14;DP=64;ExcessHet=3.01;MQRankSum=0.913;RAW_MQandDP=228169,64;ReadPosRankSum=-2.230e-01	GT:AD:DP:GQ:PL:SB	./.:36,28,0:64:99:934,0,1248,1042,1332,2374:16,20,19,9	./.
 20	10000118	.	T	<NON_REF>	.	.	END=10000210	GT:DP:GQ:MIN_DP:PL	./.:52:99:44:0,108,1620	./.
-20	10000211	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.87;DP=53;ExcessHet=3.01;MQRankSum=1.06;RAW_MQ=188569.00;ReadPosRankSum=0.703	GT:AD:DP:GQ:PL:SB	./.:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16	./.
+20	10000211	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.87;DP=53;ExcessHet=3.01;MQRankSum=1.06;RAW_MQandDP=188569,53;ReadPosRankSum=0.703	GT:AD:DP:GQ:PL:SB	./.:26,27,0:53:99:970,0,906,1049,988,2036:15,11,11,16	./.
 20	10000212	.	A	<NON_REF>	.	.	END=10000438	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.
-20	10000439	.	T	G,<NON_REF>	.	.	DP=80;ExcessHet=3.01;RAW_MQ=279076.00	GT:AD:DP:GQ:PL:SB	./.:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31	./.
+20	10000439	.	T	G,<NON_REF>	.	.	DP=80;ExcessHet=3.01;RAW_MQandDP=279076,80	GT:AD:DP:GQ:PL:SB	./.:0,80,0:80:99:2833,240,0,2833,240,2833:0,0,49,31	./.
 20	10000440	.	T	<NON_REF>	.	.	END=10000585	GT:DP:GQ:MIN_DP:PL	./.:55:99:41:0,102,1530	./.
 20	10000586	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:44:93:44:0,93,1503	./.
 20	10000587	.	G	<NON_REF>	.	.	END=10000597	GT:DP:GQ:MIN_DP:PL	./.:46:99:42:0,108,1620	./.
-20	10000598	.	T	A,<NON_REF>	.	.	DP=49;ExcessHet=3.01;RAW_MQ=149628.00	GT:AD:DP:GQ:PL:SB	./.:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30	./.
+20	10000598	.	T	A,<NON_REF>	.	.	DP=49;ExcessHet=3.01;RAW_MQandDP=149628,49	GT:AD:DP:GQ:PL:SB	./.:0,49,0:49:99:1970,147,0,1970,147,1970:0,0,19,30	./.
 20	10000599	.	T	<NON_REF>	.	.	END=10000693	GT:DP:GQ:MIN_DP:PL	./.:72:99:48:0,120,1800	./.
-20	10000694	.	G	A,<NON_REF>	.	.	BaseQRankSum=3.60;DP=82;ExcessHet=3.01;MQRankSum=-5.114e+00;RAW_MQ=194196.00;ReadPosRankSum=0.657	GT:AD:DP:GQ:PL:SB	./.:45,37,0:82:99:1037,0,1601,1173,1712,2885:25,20,18,19	./.
+20	10000694	.	G	A,<NON_REF>	.	.	BaseQRankSum=3.60;DP=82;ExcessHet=3.01;MQRankSum=-5.114e+00;RAW_MQandDP=194196,82;ReadPosRankSum=0.657	GT:AD:DP:GQ:PL:SB	./.:45,37,0:82:99:1037,0,1601,1173,1712,2885:25,20,18,19	./.
 20	10000695	.	G	<NON_REF>	.	.	END=10000757	GT:DP:GQ:MIN_DP:PL	./.:89:99:79:0,120,1800	./.
-20	10000758	.	T	A,<NON_REF>	.	.	DP=95;ExcessHet=3.01;RAW_MQ=270581.00	GT:AD:DP:GQ:PL:SB	./.:0,95,0:95:99:3867,286,0,3867,286,3867:0,0,45,50	./.
+20	10000758	.	T	A,<NON_REF>	.	.	DP=95;ExcessHet=3.01;RAW_MQandDP=270581,95	GT:AD:DP:GQ:PL:SB	./.:0,95,0:95:99:3867,286,0,3867,286,3867:0,0,45,50	./.
 20	10000759	.	A	<NON_REF>	.	.	END=10001018	GT:DP:GQ:MIN_DP:PL	./.:66:99:52:0,120,1800	./.
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@@ -153,13 +235,13 @@
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@@ -188,9 +270,9 @@
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@@ -198,35 +280,35 @@
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-20	10004223	.	A	AG,<NON_REF>	.	.	BaseQRankSum=-4.800e-01;DP=62;ExcessHet=3.01;MQRankSum=1.89;RAW_MQ=210769.00;ReadPosRankSum=0.339	GT:AD:DP:GQ:PL:SB	./.:36,11,0:47:85:85,0,982,193,1017,1210:16,20,5,6	./.
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-20	10004769	.	TAAAACTATGC	T,<NON_REF>	.	.	BaseQRankSum=1.60;DP=79;ExcessHet=3.01;MQRankSum=-6.625e+00;RAW_MQ=216626.00;ReadPosRankSum=1.88	GT:AD:DP:GQ:PL:SB	./.:37,27,0:64:99:1019,0,1471,1130,1554,2684:14,23,7,20	./.
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@@ -238,70 +320,70 @@
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-20	10008221	.	T	C,<NON_REF>	.	.	DP=80;ExcessHet=3.01;RAW_MQ=289669.00	GT:AD:DP:GQ:PL:SB	./.:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37	./.
+20	10008221	.	T	C,<NON_REF>	.	.	DP=80;ExcessHet=3.01;RAW_MQandDP=289669,80	GT:AD:DP:GQ:PL:SB	./.:0,80,0:80:99:3253,240,0,3253,240,3253:0,0,43,37	./.
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-20	10008458	.	T	G,<NON_REF>	.	.	DP=69;ExcessHet=3.01;RAW_MQ=191842.00	GT:AD:DP:GQ:PL:SB	./.:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39	./.
+20	10008458	.	T	G,<NON_REF>	.	.	DP=69;ExcessHet=3.01;RAW_MQandDP=191842,69	GT:AD:DP:GQ:PL:SB	./.:0,69,0:69:99:2683,207,0,2683,207,2683:0,0,30,39	./.
 20	10008459	.	A	<NON_REF>	.	.	END=10008732	GT:DP:GQ:MIN_DP:PL	./.:70:99:40:0,105,1575	./.
 20	10008733	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:47:94:47:0,94,1689	./.
 20	10008734	.	G	<NON_REF>	.	.	END=10008741	GT:DP:GQ:MIN_DP:PL	./.:48:99:47:0,120,1800	./.
-20	10008742	.	G	T,<NON_REF>	.	.	BaseQRankSum=3.89;DP=49;ExcessHet=3.01;MQRankSum=-1.502e+00;RAW_MQ=67874.00;ReadPosRankSum=0.190	GT:AD:DP:GQ:PL:SB	./.:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15	./.
+20	10008742	.	G	T,<NON_REF>	.	.	BaseQRankSum=3.89;DP=49;ExcessHet=3.01;MQRankSum=-1.502e+00;RAW_MQandDP=67874,49;ReadPosRankSum=0.190	GT:AD:DP:GQ:PL:SB	./.:23,26,0:49:99:744,0,580,813,658,1471:10,13,11,15	./.
 20	10008743	.	T	<NON_REF>	.	.	END=10008757	GT:DP:GQ:MIN_DP:PL	./.:46:99:42:0,99,1485	./.
-20	10008758	.	C	CA,<NON_REF>	.	.	BaseQRankSum=0.130;DP=44;ExcessHet=3.01;MQRankSum=-1.168e+00;RAW_MQ=54656.00;ReadPosRankSum=-5.200e-02	GT:AD:DP:GQ:PL:SB	./.:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15	./.
+20	10008758	.	C	CA,<NON_REF>	.	.	BaseQRankSum=0.130;DP=44;ExcessHet=3.01;MQRankSum=-1.168e+00;RAW_MQandDP=54656,44;ReadPosRankSum=-5.200e-02	GT:AD:DP:GQ:PL:SB	./.:4,31,0:35:10:721,10,0,733,102,825:3,1,16,15	./.
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-20	10008921	.	C	CA,<NON_REF>	.	.	BaseQRankSum=0.610;DP=49;ExcessHet=3.01;MQRankSum=-1.906e+00;RAW_MQ=155512.00;ReadPosRankSum=0.173	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8	./.
+20	10008921	.	C	CA,<NON_REF>	.	.	BaseQRankSum=0.610;DP=49;ExcessHet=3.01;MQRankSum=-1.906e+00;RAW_MQandDP=155512,49;ReadPosRankSum=0.173	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:18,16,0:34:99:0|1:10008921_C_CA:291,0,366,345,415,761:10,8,8,8	./.
 20	10008922	.	A	<NON_REF>	.	.	END=10008942	GT:DP:GQ:MIN_DP:PL	./.:53:99:47:0,114,1710	./.
 20	10008943	.	A	<NON_REF>	.	.	END=10008944	GT:DP:GQ:MIN_DP:PL	./.:47:78:47:0,78,1170	./.
 20	10008945	.	A	<NON_REF>	.	.	END=10008947	GT:DP:GQ:MIN_DP:PL	./.:47:81:46:0,81,1215	./.
-20	10008948	.	TA	T,<NON_REF>	.	.	BaseQRankSum=0.994;DP=52;ExcessHet=3.01;MQRankSum=2.05;RAW_MQ=138622.00;ReadPosRankSum=0.884	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15	./.
+20	10008948	.	TA	T,<NON_REF>	.	.	BaseQRankSum=0.994;DP=52;ExcessHet=3.01;MQRankSum=2.05;RAW_MQandDP=138622,52;ReadPosRankSum=0.884	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15	./.
 20	10008949	.	A	*,<NON_REF>	.	.	DP=52	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:1,0,35,15	./.
 20	10008950	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:52:99:52:0,99,1485	./.
 20	10008951	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:51:93:51:0,93,1395	./.
-20	10008952	.	CACACACACACACA	C,CCA,CCACACACACA,CCACACACACACA,<NON_REF>	.	.	BaseQRankSum=0.941;DP=59;ExcessHet=3.01;MQRankSum=1.84;RAW_MQ=154068.00;ReadPosRankSum=0.716	GT:AD:DP:GQ:PL:SB	./.:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8	./.
+20	10008952	.	CACACACACACACA	C,CCA,CCACACACACA,CCACACACACACA,<NON_REF>	.	.	BaseQRankSum=0.941;DP=59;ExcessHet=3.01;MQRankSum=1.84;RAW_MQandDP=154068,59;ReadPosRankSum=0.716	GT:AD:DP:GQ:PL:SB	./.:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8	./.
 20	10008953	.	A	*,<NON_REF>	.	.	DP=59	GT:AD:DP:GQ:PL:SB	./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8	./.
 20	10008954	.	C	*,<NON_REF>	.	.	DP=59	GT:AD:DP:GQ:PL:SB	./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8	./.
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@@ -318,23 +400,23 @@
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-20	10009227	.	A	G,<NON_REF>	.	.	BaseQRankSum=-2.220e+00;DP=62;ExcessHet=3.01;MQRankSum=1.43;RAW_MQ=202588.00;ReadPosRankSum=-1.159e+00	GT:AD:DP:GQ:PL:SB	./.:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20	./.
+20	10009227	.	A	G,<NON_REF>	.	.	BaseQRankSum=-2.220e+00;DP=62;ExcessHet=3.01;MQRankSum=1.43;RAW_MQandDP=202588,62;ReadPosRankSum=-1.159e+00	GT:AD:DP:GQ:PL:SB	./.:23,39,0:62:99:1398,0,740,1468,857,2325:16,7,19,20	./.
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-20	10009246	.	A	G,<NON_REF>	.	.	DP=77;ExcessHet=3.01;RAW_MQ=242208.00	GT:AD:DP:GQ:PL:SB	./.:0,77,0:77:99:3031,231,0,3031,231,3031:0,0,42,35	./.
+20	10009246	.	A	G,<NON_REF>	.	.	DP=77;ExcessHet=3.01;RAW_MQandDP=242208,77	GT:AD:DP:GQ:PL:SB	./.:0,77,0:77:99:3031,231,0,3031,231,3031:0,0,42,35	./.
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-20	10009400	.	T	A,<NON_REF>	.	.	DP=74;ExcessHet=3.01;RAW_MQ=266400.00	GT:AD:DP:GQ:PL:SB	./.:0,74,0:74:99:3027,223,0,3027,223,3027:0,0,39,35	./.
+20	10009400	.	T	A,<NON_REF>	.	.	DP=74;ExcessHet=3.01;RAW_MQandDP=266400,74	GT:AD:DP:GQ:PL:SB	./.:0,74,0:74:99:3027,223,0,3027,223,3027:0,0,39,35	./.
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-20	10009512	.	C	G,<NON_REF>	.	.	DP=77;ExcessHet=3.01;RAW_MQ=263240.00	GT:AD:DP:GQ:PL:SB	./.:0,77,0:77:99:3068,231,0,3068,231,3068:0,0,30,47	./.
+20	10009512	.	C	G,<NON_REF>	.	.	DP=77;ExcessHet=3.01;RAW_MQandDP=263240,77	GT:AD:DP:GQ:PL:SB	./.:0,77,0:77:99:3068,231,0,3068,231,3068:0,0,30,47	./.
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-20	10009719	.	A	G,<NON_REF>	.	.	DP=59;ExcessHet=3.01;RAW_MQ=207410.00	GT:AD:DP:GQ:PL:SB	./.:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33	./.
+20	10009719	.	A	G,<NON_REF>	.	.	DP=59;ExcessHet=3.01;RAW_MQandDP=207410,59	GT:AD:DP:GQ:PL:SB	./.:0,59,0:59:99:1924,175,0,1924,175,1924:0,0,26,33	./.
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-20	10009795	.	A	G,<NON_REF>	.	.	DP=47;ExcessHet=3.01;RAW_MQ=166969.00	GT:AD:DP:GQ:PL:SB	./.:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31	./.
+20	10009795	.	A	G,<NON_REF>	.	.	DP=47;ExcessHet=3.01;RAW_MQandDP=166969,47	GT:AD:DP:GQ:PL:SB	./.:0,47,0:47:99:1909,141,0,1909,141,1909:0,0,16,31	./.
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-20	10009842	.	G	GAA,<NON_REF>	.	.	BaseQRankSum=0.872;DP=51;ExcessHet=3.01;MQRankSum=-6.030e-01;RAW_MQ=150092.00;ReadPosRankSum=1.72	GT:AD:DP:GQ:PL:SB	./.:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7	./.
+20	10009842	.	G	GAA,<NON_REF>	.	.	BaseQRankSum=0.872;DP=51;ExcessHet=3.01;MQRankSum=-6.030e-01;RAW_MQandDP=150092,51;ReadPosRankSum=1.72	GT:AD:DP:GQ:PL:SB	./.:19,15,0:34:99:570,0,690,629,738,1367:9,10,8,7	./.
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-20	10009844	.	G	A,<NON_REF>	.	.	BaseQRankSum=1.05;DP=51;ExcessHet=3.01;MQRankSum=0.975;RAW_MQ=147168.00;ReadPosRankSum=-1.555e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10	./.
+20	10009844	.	G	A,<NON_REF>	.	.	BaseQRankSum=1.05;DP=51;ExcessHet=3.01;MQRankSum=0.975;RAW_MQandDP=147168,51;ReadPosRankSum=-1.555e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:16,19,0:35:99:0|1:10009844_G_A:690,0,586,739,644,1382:8,8,9,10	./.
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@@ -343,13 +425,13 @@
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-20	10009871	.	A	G,<NON_REF>	.	.	BaseQRankSum=-8.030e-01;DP=60;ExcessHet=3.01;MQRankSum=1.50;RAW_MQ=154737.00;ReadPosRankSum=1.54	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10	./.
+20	10009871	.	A	G,<NON_REF>	.	.	BaseQRankSum=-8.030e-01;DP=60;ExcessHet=3.01;MQRankSum=1.50;RAW_MQandDP=154737,60;ReadPosRankSum=1.54	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:17,19,0:36:99:0|1:10009844_G_A:687,0,594,739,652,1391:10,7,9,10	./.
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-20	10009875	.	A	G,AGGGAGG,<NON_REF>	.	.	BaseQRankSum=0.378;DP=57;ExcessHet=3.01;MQRankSum=1.36;RAW_MQ=143937.00;ReadPosRankSum=1.04	GT:AD:DP:GQ:PL:SB	./.:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16	./.
+20	10009875	.	A	G,AGGGAGG,<NON_REF>	.	.	BaseQRankSum=0.378;DP=57;ExcessHet=3.01;MQRankSum=1.36;RAW_MQandDP=143937,57;ReadPosRankSum=1.04	GT:AD:DP:GQ:PL:SB	./.:2,15,13,0:30:99:2407,645,533,697,0,574,1881,655,700,1805:2,0,12,16	./.
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-20	10009879	.	A	G,<NON_REF>	.	.	BaseQRankSum=1.53;DP=49;ExcessHet=3.01;MQRankSum=1.57;RAW_MQ=120661.00;ReadPosRankSum=1.11	GT:AD:DP:GQ:PL:SB	./.:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32	./.
+20	10009879	.	A	G,<NON_REF>	.	.	BaseQRankSum=1.53;DP=49;ExcessHet=3.01;MQRankSum=1.57;RAW_MQandDP=120661,49;ReadPosRankSum=1.11	GT:AD:DP:GQ:PL:SB	./.:2,47,0:49:99:2273,150,0,2276,154,2279:2,0,15,32	./.
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-20	10009883	.	A	G,<NON_REF>	.	.	DP=49;ExcessHet=3.01;RAW_MQ=129338.00	GT:AD:DP:GQ:PL:SB	./.:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32	./.
+20	10009883	.	A	G,<NON_REF>	.	.	DP=49;ExcessHet=3.01;RAW_MQandDP=129338,49	GT:AD:DP:GQ:PL:SB	./.:0,47,0:47:99:2180,147,0,2180,147,2181:0,0,15,32	./.
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@@ -360,27 +442,27 @@
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-20	10010393	.	T	G,<NON_REF>	.	.	BaseQRankSum=-3.351e+00;DP=79;ExcessHet=3.01;MQRankSum=-1.284e+00;RAW_MQ=278882.00;ReadPosRankSum=-1.738e+00	GT:AD:DP:GQ:PL:SB	./.:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24	./.
+20	10010393	.	T	G,<NON_REF>	.	.	BaseQRankSum=-3.351e+00;DP=79;ExcessHet=3.01;MQRankSum=-1.284e+00;RAW_MQandDP=278882,79;ReadPosRankSum=-1.738e+00	GT:AD:DP:GQ:PL:SB	./.:36,43,0:79:99:1493,0,1230,1601,1359,2961:24,12,19,24	./.
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-20	10010536	.	G	GA,<NON_REF>	.	.	DP=85;ExcessHet=3.01;RAW_MQ=322900.00	GT:AD:DP:GQ:PL:SB	./.:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43	./.
+20	10010536	.	G	GA,<NON_REF>	.	.	DP=85;ExcessHet=3.01;RAW_MQandDP=322900,85	GT:AD:DP:GQ:PL:SB	./.:0,79,0:79:99:2500,243,0,2500,244,2500:0,0,36,43	./.
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@@ -533,11 +615,11 @@
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@@ -555,7 +637,7 @@
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@@ -675,7 +757,7 @@
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@@ -698,7 +780,7 @@
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@@ -741,20 +823,20 @@
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@@ -765,7 +847,7 @@
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@@ -786,20 +868,20 @@
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+20	10026357	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.700e+00;DP=63;ExcessHet=3.01;MQRankSum=-1.480e-01;RAW_MQandDP=215117,63;ReadPosRankSum=-7.600e-02	GT:AD:DP:GQ:PL:SB	./.:28,35,0:63:99:1195,0,932,1279,1037,2316:10,18,20,15	./.
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-20	10026794	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.83;DP=52;ExcessHet=3.01;MQRankSum=-7.190e-01;RAW_MQ=184441.00;ReadPosRankSum=-5.330e-01	GT:AD:DP:GQ:PL:SB	./.:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18	./.
+20	10026794	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.83;DP=52;ExcessHet=3.01;MQRankSum=-7.190e-01;RAW_MQandDP=184441,52;ReadPosRankSum=-5.330e-01	GT:AD:DP:GQ:PL:SB	./.:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18	./.
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-20	10027234	.	A	ATTAG,<NON_REF>	.	.	BaseQRankSum=-4.060e-01;DP=72;ExcessHet=3.01;MQRankSum=-8.450e-01;RAW_MQ=236651.00;ReadPosRankSum=-9.790e-01	GT:AD:DP:GQ:PL:SB	./.:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20	./.
+20	10027234	.	A	ATTAG,<NON_REF>	.	.	BaseQRankSum=-4.060e-01;DP=72;ExcessHet=3.01;MQRankSum=-8.450e-01;RAW_MQandDP=236651,72;ReadPosRankSum=-9.790e-01	GT:AD:DP:GQ:PL:SB	./.:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20	./.
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+20	10027872	.	A	G,<NON_REF>	.	.	BaseQRankSum=-5.491e+00;DP=85;ExcessHet=3.01;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.05	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:16,24,26,19	./.
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-20	10028867	.	A	ATG,<NON_REF>	.	.	BaseQRankSum=-8.740e-01;DP=92;ExcessHet=3.01;MQRankSum=2.71;RAW_MQ=338841.00;ReadPosRankSum=0.364	GT:AD:DP:GQ:PL:SB	./.:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21	./.
+20	10028867	.	A	ATG,<NON_REF>	.	.	BaseQRankSum=-8.740e-01;DP=92;ExcessHet=3.01;MQRankSum=2.71;RAW_MQandDP=338841,92;ReadPosRankSum=0.364	GT:AD:DP:GQ:PL:SB	./.:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21	./.
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-20	10030188	.	T	A,<NON_REF>	.	.	BaseQRankSum=0.711;ClippingRankSum=0.00;DP=419;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=1505641.00;ReadPosRankSum=1.23	GT:AD:DP:GQ:PL:SB	./.:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24	./././././././././.:294,41,0:335:28:798,0,28,126,272,464,716,1054,1545,2400,9304,932,150,198,323,504,748,1081,1569,2421,9323,1082,320,394,555,788,1114,1596,2445,9344,1252,517,627,839,1153,1628,2472,9367,1449,749,911,1204,1668,2505,9395,1681,1033,1276,1719,2544,9427,1965,1398,1791,2595,9467,2330,1913,2667,9518,2845,2789,9589,3721,9712,10644:130,164,23,18
+20	10030188	.	T	A,<NON_REF>	.	.	BaseQRankSum=0.711;ClippingRankSum=0.00;DP=419;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=1216800.00;RAW_MQandDP=288841,81;ReadPosRankSum=1.23	GT:AD:DP:GQ:PL:SB	./.:42,39,0:81:99:1401,0,1524,1527,1641,3168:24,18,15,24	./././././././././.:294,41,0:335:28:798,0,28,126,272,464,716,1054,1545,2400,9304,932,150,198,323,504,748,1081,1569,2421,9323,1082,320,394,555,788,1114,1596,2445,9344,1252,517,627,839,1153,1628,2472,9367,1449,749,911,1204,1668,2505,9395,1681,1033,1276,1719,2544,9427,1965,1398,1791,2595,9467,2330,1913,2667,9518,2845,2789,9589,3721,9712,10644:130,164,23,18
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@@ -812,23 +894,23 @@
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-20	10031254	.	A	AT,<NON_REF>	.	.	BaseQRankSum=-9.100e-02;DP=87;ExcessHet=3.01;MQRankSum=0.017;RAW_MQ=309510.00;ReadPosRankSum=0.495	GT:AD:DP:GQ:PL:SB	./.:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22	./.
+20	10031254	.	A	AT,<NON_REF>	.	.	BaseQRankSum=-9.100e-02;DP=87;ExcessHet=3.01;MQRankSum=0.017;RAW_MQandDP=309510,87;ReadPosRankSum=0.495	GT:AD:DP:GQ:PL:SB	./.:38,47,0:85:99:1501,0,1159,1616,1300,2916:27,11,25,22	./.
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-20	10031342	.	G	A,<NON_REF>	.	.	BaseQRankSum=1.83;DP=93;ExcessHet=3.01;MQRankSum=-8.660e-01;RAW_MQ=332041.00;ReadPosRankSum=-1.200e-02	GT:AD:DP:GQ:PL:SB	./.:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21	./.
+20	10031342	.	G	A,<NON_REF>	.	.	BaseQRankSum=1.83;DP=93;ExcessHet=3.01;MQRankSum=-8.660e-01;RAW_MQandDP=332041,93;ReadPosRankSum=-1.200e-02	GT:AD:DP:GQ:PL:SB	./.:41,52,0:93:99:1863,0,1375,1986,1531,3517:22,19,31,21	./.
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-20	10031798	.	G	A,<NON_REF>	.	.	DP=104;ExcessHet=3.01;RAW_MQ=369410.00	GT:AD:DP:GQ:PL:SB	./.:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47	./.
+20	10031798	.	G	A,<NON_REF>	.	.	DP=104;ExcessHet=3.01;RAW_MQandDP=369410,104	GT:AD:DP:GQ:PL:SB	./.:0,104,0:104:99:4325,313,0,4325,313,4325:0,0,57,47	./.
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-20	10031827	.	C	T,<NON_REF>	.	.	BaseQRankSum=3.55;DP=108;ExcessHet=3.01;MQRankSum=-9.450e-01;RAW_MQ=386569.00;ReadPosRankSum=-1.396e+00	GT:AD:DP:GQ:PL:SB	./.:52,56,0:108:99:2033,0,1798,2189,1966,4155:32,20,29,27	./.
+20	10031827	.	C	T,<NON_REF>	.	.	BaseQRankSum=3.55;DP=108;ExcessHet=3.01;MQRankSum=-9.450e-01;RAW_MQandDP=386569,108;ReadPosRankSum=-1.396e+00	GT:AD:DP:GQ:PL:SB	./.:52,56,0:108:99:2033,0,1798,2189,1966,4155:32,20,29,27	./.
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-20	10032094	.	G	A,<NON_REF>	.	.	BaseQRankSum=5.49;DP=83;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=298800.00;ReadPosRankSum=-5.790e-01	GT:AD:DP:GQ:PL:SB	./.:47,36,0:83:99:1249,0,1497,1390,1605,2995:14,33,16,20	./.
+20	10032094	.	G	A,<NON_REF>	.	.	BaseQRankSum=5.49;DP=83;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=298800,83;ReadPosRankSum=-5.790e-01	GT:AD:DP:GQ:PL:SB	./.:47,36,0:83:99:1249,0,1497,1390,1605,2995:14,33,16,20	./.
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-20	10032413	.	T	G,<NON_REF>	.	.	BaseQRankSum=-4.498e+00;ClippingRankSum=0.00;DP=407;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=1460738.00;ReadPosRankSum=0.742	GT:AD:DP:GQ:PL:SB	./.:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11	./././././././././.:287,49,0:336:1:944,0,1,81,212,391,630,955,1430,2263,9275,1075,147,167,273,439,669,988,1458,2288,9298,1222,313,359,500,716,1026,1491,2316,9323,1388,505,585,777,1074,1530,2349,9351,1580,732,863,1135,1577,2388,9384,1807,1009,1221,1638,2435,9423,2084,1367,1724,2496,9470,2442,1870,2582,9531,2945,2728,9617,3803,9763,10838:145,142,30,19
+20	10032413	.	T	G,<NON_REF>	.	.	BaseQRankSum=-4.498e+00;ClippingRankSum=0.00;DP=407;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=1227600.00;RAW_MQandDP=233138,66;ReadPosRankSum=0.742	GT:AD:DP:GQ:PL:SB	./.:35,31,0:66:99:898,0,1277,1003,1371,2374:15,20,20,11	./././././././././.:287,49,0:336:1:944,0,1,81,212,391,630,955,1430,2263,9275,1075,147,167,273,439,669,988,1458,2288,9298,1222,313,359,500,716,1026,1491,2316,9323,1388,505,585,777,1074,1530,2349,9351,1580,732,863,1135,1577,2388,9384,1807,1009,1221,1638,2435,9423,2084,1367,1724,2496,9470,2442,1870,2582,9531,2945,2728,9617,3803,9763,10838:145,142,30,19
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-20	10032882	.	A	T,<NON_REF>	.	.	BaseQRankSum=-3.697e+00;DP=75;ExcessHet=3.01;MQRankSum=-1.014e+00;RAW_MQ=267241.00;ReadPosRankSum=0.626	GT:AD:DP:GQ:PL:SB	./.:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14	./.
+20	10032882	.	A	T,<NON_REF>	.	.	BaseQRankSum=-3.697e+00;DP=75;ExcessHet=3.01;MQRankSum=-1.014e+00;RAW_MQandDP=267241,75;ReadPosRankSum=0.626	GT:AD:DP:GQ:PL:SB	./.:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14	./.
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-20	10032972	.	C	CAT,<NON_REF>	.	.	BaseQRankSum=-3.540e-01;DP=65;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQ=231241.00;ReadPosRankSum=-1.232e+00	GT:AD:DP:GQ:PL:SB	./.:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19	./.
+20	10032972	.	C	CAT,<NON_REF>	.	.	BaseQRankSum=-3.540e-01;DP=65;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232e+00	GT:AD:DP:GQ:PL:SB	./.:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19	./.
 20	10032973	.	T	<NON_REF>	.	.	END=10033636	GT:DP:GQ:MIN_DP:PL	./.:78:99:50:0,120,1800	./.
 20	10033637	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:58:97:58:0,97,2210	./.
 20	10033638	.	C	<NON_REF>	.	.	END=10033758	GT:DP:GQ:MIN_DP:PL	./.:85:99:53:0,120,1800	./.
@@ -836,7 +918,7 @@
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-20	10034306	.	T	C,<NON_REF>	.	.	BaseQRankSum=-3.661e+00;DP=76;ExcessHet=3.01;MQRankSum=1.15;RAW_MQ=268610.00;ReadPosRankSum=0.539	GT:AD:DP:GQ:PL:SB	./.:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15	./.
+20	10034306	.	T	C,<NON_REF>	.	.	BaseQRankSum=-3.661e+00;DP=76;ExcessHet=3.01;MQRankSum=1.15;RAW_MQandDP=268610,76;ReadPosRankSum=0.539	GT:AD:DP:GQ:PL:SB	./.:46,29,0:75:99:811,0,1593,950,1680,2630:24,22,14,15	./.
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 20	10035250	.	A	<NON_REF>	.	.	END=10036106	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.
@@ -853,7 +935,7 @@
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 20	10036311	.	C	<NON_REF>	.	.	END=10036929	GT:DP:GQ:MIN_DP:PL	./.:76:99:43:0,113,1513	./.
-20	10036930	.	CGATAGCCCTAGCCCTAGATA	C,<NON_REF>	.	.	BaseQRankSum=0.200;DP=93;ExcessHet=3.01;MQRankSum=-4.048e+00;RAW_MQ=274847.00;ReadPosRankSum=0.460	GT:AD:DP:GQ:PL:SB	./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14	./.
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@@ -888,11 +970,11 @@
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@@ -903,41 +985,41 @@
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@@ -969,7 +1051,7 @@
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@@ -977,15 +1059,15 @@
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@@ -1174,27 +1256,27 @@
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+20	10087394	.	T	G,<NON_REF>	.	.	BaseQRankSum=-2.340e+00;DP=84;ExcessHet=3.01;MQRankSum=1.21;RAW_MQandDP=299641,84;ReadPosRankSum=0.885	GT:AD:DP:GQ:PL:SB	./.:35,49,0:84:99:1717,0,1186,1823,1334,3156:21,14,24,25	./.
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+20	10087804	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.94;DP=100;ExcessHet=3.01;MQRankSum=2.62;RAW_MQandDP=369310,100;ReadPosRankSum=0.341	GT:AD:DP:GQ:PL:SB	./.:50,50,0:100:99:1648,0,1511,1797,1661,3458:33,17,28,22	./.
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-20	10087820	.	CAG	C,CAGAG,<NON_REF>	.	.	BaseQRankSum=-1.974e+00;DP=99;ExcessHet=3.01;MQRankSum=0.422;RAW_MQ=362700.00;ReadPosRankSum=-3.570e-01	GT:AD:DP:GQ:PL:SB	./.:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10	./.
+20	10087820	.	CAG	C,CAGAG,<NON_REF>	.	.	BaseQRankSum=-1.974e+00;DP=99;ExcessHet=3.01;MQRankSum=0.422;RAW_MQandDP=362700,99;ReadPosRankSum=-3.570e-01	GT:AD:DP:GQ:PL:SB	./.:35,0,18,0:53:99:466,669,2577,0,1197,1168,661,2237,1238,2189:17,18,8,10	./.
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@@ -1202,17 +1284,17 @@
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+20	10088063	.	C	T,<NON_REF>	.	.	BaseQRankSum=3.41;DP=93;ExcessHet=3.01;MQRankSum=0.515;RAW_MQandDP=327579,93;ReadPosRankSum=0.285	GT:AD:DP:GQ:PL:SB	./.:49,44,0:93:99:1446,0,1403,1592,1535,3128:24,25,18,26	./.
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-20	10088699	.	C	T,<NON_REF>	.	.	BaseQRankSum=3.80;DP=63;ExcessHet=3.01;MQRankSum=-3.140e+00;RAW_MQ=199738.00;ReadPosRankSum=-1.456e+00	GT:AD:DP:GQ:PL:SB	./.:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7	./.
+20	10088699	.	C	T,<NON_REF>	.	.	BaseQRankSum=3.80;DP=63;ExcessHet=3.01;MQRankSum=-3.140e+00;RAW_MQandDP=199738,63;ReadPosRankSum=-1.456e+00	GT:AD:DP:GQ:PL:SB	./.:36,26,0:62:99:805,0,1088,913,1166,2079:15,21,19,7	./.
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-20	10088747	.	A	G,<NON_REF>	.	.	BaseQRankSum=-3.877e+00;DP=55;ExcessHet=3.01;MQRankSum=-4.907e+00;RAW_MQ=146239.00;ReadPosRankSum=9.000e-03	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11	./.
+20	10088747	.	A	G,<NON_REF>	.	.	BaseQRankSum=-3.877e+00;DP=55;ExcessHet=3.01;MQRankSum=-4.907e+00;RAW_MQandDP=146239,55;ReadPosRankSum=9.000e-03	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:25,29,0:54:99:0|1:10088730_G_A:1140,0,995,1219,1085,2304:10,15,18,11	./.
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-20	10088799	.	G	A,<NON_REF>	.	.	BaseQRankSum=5.50;DP=53;ExcessHet=3.01;MQRankSum=-2.498e+00;RAW_MQ=150040.00;ReadPosRankSum=1.08	GT:AD:DP:GQ:PL:SB	./.:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19	./.
+20	10088799	.	G	A,<NON_REF>	.	.	BaseQRankSum=5.50;DP=53;ExcessHet=3.01;MQRankSum=-2.498e+00;RAW_MQandDP=150040,53;ReadPosRankSum=1.08	GT:AD:DP:GQ:PL:SB	./.:22,31,0:53:99:1047,0,617,1114,711,1824:14,8,12,19	./.
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@@ -1231,13 +1313,13 @@
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+20	10088895	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.46;DP=41;ExcessHet=3.01;MQRankSum=0.577;RAW_MQandDP=134450,41;ReadPosRankSum=1.30	GT:AD:DP:GQ:PL:SB	./.:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10	./.
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-20	10088968	.	C	CAAA,<NON_REF>	.	.	BaseQRankSum=0.552;DP=62;ExcessHet=3.01;MQRankSum=-4.750e+00;RAW_MQ=177808.00;ReadPosRankSum=2.42	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:16,14,14,9	./.
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-20	10088980	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.585e+00;DP=68;ExcessHet=3.01;MQRankSum=-5.232e+00;RAW_MQ=176353.00;ReadPosRankSum=1.29	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16	./.
+20	10088980	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.585e+00;DP=68;ExcessHet=3.01;MQRankSum=-5.232e+00;RAW_MQandDP=176353,68;ReadPosRankSum=1.29	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:19,18,15,16	./.
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-20	10088985	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.920e-01;DP=74;ExcessHet=3.01;MQRankSum=-5.248e+00;RAW_MQ=191764.00;ReadPosRankSum=1.23	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17	./.
+20	10088985	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.920e-01;DP=74;ExcessHet=3.01;MQRankSum=-5.248e+00;RAW_MQandDP=191764,74;ReadPosRankSum=1.23	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:22,20,15,17	./.
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@@ -1251,37 +1333,37 @@
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-20	10089441	.	A	G,<NON_REF>	.	.	BaseQRankSum=-4.885e+00;DP=76;ExcessHet=3.01;MQRankSum=-9.480e-01;RAW_MQ=270841.00;ReadPosRankSum=-1.560e-01	GT:AD:DP:GQ:PL:SB	./.:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25	./.
+20	10089441	.	A	G,<NON_REF>	.	.	BaseQRankSum=-4.885e+00;DP=76;ExcessHet=3.01;MQRankSum=-9.480e-01;RAW_MQandDP=270841,76;ReadPosRankSum=-1.560e-01	GT:AD:DP:GQ:PL:SB	./.:37,39,0:76:99:1208,0,1313,1319,1430,2749:19,18,14,25	./.
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-20	10089525	.	C	T,<NON_REF>	.	.	BaseQRankSum=5.86;DP=81;ExcessHet=3.01;MQRankSum=1.53;RAW_MQ=286610.00;ReadPosRankSum=0.862	GT:AD:DP:GQ:PL:SB	./.:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23	./.
+20	10089525	.	C	T,<NON_REF>	.	.	BaseQRankSum=5.86;DP=81;ExcessHet=3.01;MQRankSum=1.53;RAW_MQandDP=286610,81;ReadPosRankSum=0.862	GT:AD:DP:GQ:PL:SB	./.:38,43,0:81:99:1577,0,1088,1691,1217,2908:22,16,20,23	./.
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-20	10090289	.	CAA	C,CA,<NON_REF>	.	.	BaseQRankSum=0.441;DP=80;ExcessHet=3.01;MQRankSum=1.39;RAW_MQ=287682.00;ReadPosRankSum=0.048	GT:AD:DP:GQ:PL:SB	./.:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13	./.
+20	10090289	.	CAA	C,CA,<NON_REF>	.	.	BaseQRankSum=0.441;DP=80;ExcessHet=3.01;MQRankSum=1.39;RAW_MQandDP=287682,80;ReadPosRankSum=0.048	GT:AD:DP:GQ:PL:SB	./.:14,4,20,0:38:99:422,360,986,0,261,230,477,867,348,928:7,7,11,13	./.
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+20	10090764	.	A	G,<NON_REF>	.	.	BaseQRankSum=-2.659e+00;DP=63;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=226800,63;ReadPosRankSum=1.21	GT:AD:DP:GQ:PL:SB	./.:34,29,0:63:99:869,0,1207,972,1294,2265:12,22,14,15	./.
 20	10090765	.	A	<NON_REF>	.	.	END=10090969	GT:DP:GQ:MIN_DP:PL	./.:75:99:65:0,120,1800	./.
-20	10090970	.	T	C,<NON_REF>	.	.	BaseQRankSum=-4.840e-01;DP=69;ExcessHet=3.01;MQRankSum=1.51;RAW_MQ=243938.00;ReadPosRankSum=-7.200e-02	GT:AD:DP:GQ:PL:SB	./.:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16	./.
+20	10090970	.	T	C,<NON_REF>	.	.	BaseQRankSum=-4.840e-01;DP=69;ExcessHet=3.01;MQRankSum=1.51;RAW_MQandDP=243938,69;ReadPosRankSum=-7.200e-02	GT:AD:DP:GQ:PL:SB	./.:33,36,0:69:99:1286,0,1092,1384,1201,2585:20,13,20,16	./.
 20	10090971	.	C	<NON_REF>	.	.	END=10091213	GT:DP:GQ:MIN_DP:PL	./.:61:99:49:0,120,1800	./.
-20	10091214	.	C	T,<NON_REF>	.	.	BaseQRankSum=0.361;DP=70;ExcessHet=3.01;MQRankSum=-9.160e-01;RAW_MQ=249769.00;ReadPosRankSum=-3.500e-02	GT:AD:DP:GQ:PL:SB	./.:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24	./.
+20	10091214	.	C	T,<NON_REF>	.	.	BaseQRankSum=0.361;DP=70;ExcessHet=3.01;MQRankSum=-9.160e-01;RAW_MQandDP=249769,70;ReadPosRankSum=-3.500e-02	GT:AD:DP:GQ:PL:SB	./.:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24	./.
 20	10091215	.	C	<NON_REF>	.	.	END=10092414	GT:DP:GQ:MIN_DP:PL	./.:69:99:46:0,120,1800	./.
-20	10092415	.	A	G,<NON_REF>	.	.	BaseQRankSum=-6.731e+00;DP=101;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=363600.00;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	./.:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25	./.
+20	10092415	.	A	G,<NON_REF>	.	.	BaseQRankSum=-6.731e+00;DP=101;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=363600,101;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	./.:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25	./.
 20	10092416	.	G	<NON_REF>	.	.	END=10092926	GT:DP:GQ:MIN_DP:PL	./.:80:99:60:0,120,1800	./.
-20	10092927	.	G	T,<NON_REF>	.	.	BaseQRankSum=-2.507e+00;DP=73;ExcessHet=3.01;MQRankSum=-3.009e+00;RAW_MQ=257282.00;ReadPosRankSum=-2.200e-01	GT:AD:DP:GQ:PL:SB	./.:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13	./.
+20	10092927	.	G	T,<NON_REF>	.	.	BaseQRankSum=-2.507e+00;DP=73;ExcessHet=3.01;MQRankSum=-3.009e+00;RAW_MQandDP=257282,73;ReadPosRankSum=-2.200e-01	GT:AD:DP:GQ:PL:SB	./.:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13	./.
 20	10092928	.	T	<NON_REF>	.	.	END=10093567	GT:DP:GQ:MIN_DP:PL	./.:79:99:57:0,120,1800	./.
-20	10093568	.	GTT	G,GT,GTTT,<NON_REF>	.	.	BaseQRankSum=0.426;DP=59;ExcessHet=3.01;MQRankSum=0.410;RAW_MQ=203561.00;ReadPosRankSum=1.26	GT:AD:DP:GQ:PL:SB	./.:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15	./.
+20	10093568	.	GTT	G,GT,GTTT,<NON_REF>	.	.	BaseQRankSum=0.426;DP=59;ExcessHet=3.01;MQRankSum=0.410;RAW_MQandDP=203561,59;ReadPosRankSum=1.26	GT:AD:DP:GQ:PL:SB	./.:17,4,17,4,0:42:99:364,329,1122,0,430,386,377,710,293,909,431,838,449,780,885:7,10,10,15	./.
 20	10093569	.	T	*,<NON_REF>	.	.	DP=59	GT:AD:DP:GQ:PL:SB	./.:17,17,0:42:99:364,0,386,431,449,885:7,10,10,15	./.
 20	10093570	.	T	*,<NON_REF>	.	.	DP=59	GT:AD:DP:GQ:PL:SB	./.:17,17,0:42:99:364,0,386,431,449,885:7,10,10,15	./.
 20	10093571	.	T	<NON_REF>	.	.	END=10093922	GT:DP:GQ:MIN_DP:PL	./.:62:99:51:0,99,1485	./.
-20	10093923	.	T	A,<NON_REF>	.	.	BaseQRankSum=-6.670e-01;DP=67;ExcessHet=3.01;MQRankSum=0.358;RAW_MQ=234704.00;ReadPosRankSum=-1.583e+00	GT:AD:DP:GQ:PL:SB	./.:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17	./.
+20	10093923	.	T	A,<NON_REF>	.	.	BaseQRankSum=-6.670e-01;DP=67;ExcessHet=3.01;MQRankSum=0.358;RAW_MQandDP=234704,67;ReadPosRankSum=-1.583e+00	GT:AD:DP:GQ:PL:SB	./.:35,32,0:67:99:1104,0,1257,1209,1353,2563:18,17,15,17	./.
 20	10093924	.	G	<NON_REF>	.	.	END=10094250	GT:DP:GQ:MIN_DP:PL	./.:66:99:53:0,120,1800	./.
-20	10094251	.	T	A,<NON_REF>	.	.	BaseQRankSum=0.251;DP=62;ExcessHet=3.01;MQRankSum=0.00;RAW_MQ=223200.00;ReadPosRankSum=1.81	GT:AD:DP:GQ:PL:SB	./.:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13	./.
+20	10094251	.	T	A,<NON_REF>	.	.	BaseQRankSum=0.251;DP=62;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=223200,62;ReadPosRankSum=1.81	GT:AD:DP:GQ:PL:SB	./.:26,36,0:62:99:1299,0,781,1376,889,2265:10,16,23,13	./.
 20	10094252	.	C	<NON_REF>	.	.	END=10094581	GT:DP:GQ:MIN_DP:PL	./.:68:99:46:0,117,1755	./.
-20	10094582	.	A	G,<NON_REF>	.	.	BaseQRankSum=-1.388e+00;DP=69;ExcessHet=3.01;MQRankSum=1.27;RAW_MQ=243410.00;ReadPosRankSum=-1.800e-02	GT:AD:DP:GQ:PL:SB	./.:39,30,0:69:99:952,0,1350,1070,1440,2510:20,19,16,14	./.
+20	10094582	.	A	G,<NON_REF>	.	.	BaseQRankSum=-1.388e+00;DP=69;ExcessHet=3.01;MQRankSum=1.27;RAW_MQandDP=243410,69;ReadPosRankSum=-1.800e-02	GT:AD:DP:GQ:PL:SB	./.:39,30,0:69:99:952,0,1350,1070,1440,2510:20,19,16,14	./.
 20	10094583	.	T	<NON_REF>	.	.	END=10094773	GT:DP:GQ:MIN_DP:PL	./.:78:99:67:0,120,1800	./.
-20	10094774	.	C	T,<NON_REF>	.	.	BaseQRankSum=-7.840e-01;DP=75;ExcessHet=3.01;MQRankSum=0.962;RAW_MQ=267241.00;ReadPosRankSum=0.197	GT:AD:DP:GQ:PL:SB	./.:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14	./.
+20	10094774	.	C	T,<NON_REF>	.	.	BaseQRankSum=-7.840e-01;DP=75;ExcessHet=3.01;MQRankSum=0.962;RAW_MQandDP=267241,75;ReadPosRankSum=0.197	GT:AD:DP:GQ:PL:SB	./.:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14	./.
 20	10094775	.	A	<NON_REF>	.	.	END=10095431	GT:DP:GQ:MIN_DP:PL	./.:77:99:63:0,120,1800	./.
-20	10095432	.	GTGATGATGA	G,<NON_REF>	.	.	BaseQRankSum=1.26;DP=77;ExcessHet=3.01;MQRankSum=-4.431e+00;RAW_MQ=227748.00;ReadPosRankSum=0.396	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
+20	10095432	.	GTGATGATGA	G,<NON_REF>	.	.	BaseQRankSum=1.27;DP=77;ExcessHet=3.01;MQRankSum=-4.431e+00;RAW_MQandDP=227748,77;ReadPosRankSum=0.396	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
 20	10095433	.	T	*,<NON_REF>	.	.	DP=77	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
 20	10095434	.	G	*,<NON_REF>	.	.	DP=77	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
 20	10095435	.	A	*,<NON_REF>	.	.	DP=77	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
@@ -1292,29 +1374,29 @@
 20	10095440	.	G	*,<NON_REF>	.	.	DP=77	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
 20	10095441	.	A	*,<NON_REF>	.	.	DP=77	GT:AD:DP:GQ:PL:SB	./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11	./.
 20	10095442	.	T	<NON_REF>	.	.	END=10095740	GT:DP:GQ:MIN_DP:PL	./.:80:99:64:0,120,1800	./.
-20	10095741	.	A	G,<NON_REF>	.	.	BaseQRankSum=-5.340e-01;DP=71;ExcessHet=3.01;MQRankSum=-2.313e+00;RAW_MQ=233528.00;ReadPosRankSum=-5.000e-01	GT:AD:DP:GQ:PL:SB	./.:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16	./.
+20	10095741	.	A	G,<NON_REF>	.	.	BaseQRankSum=-5.340e-01;DP=71;ExcessHet=3.01;MQRankSum=-2.313e+00;RAW_MQandDP=233528,71;ReadPosRankSum=-5.000e-01	GT:AD:DP:GQ:PL:SB	./.:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16	./.
 20	10095742	.	G	<NON_REF>	.	.	END=10096292	GT:DP:GQ:MIN_DP:PL	./.:73:99:63:0,120,1800	./.
-20	10096293	.	C	T,<NON_REF>	.	.	BaseQRankSum=4.66;DP=75;ExcessHet=3.01;MQRankSum=1.40;RAW_MQ=257261.00;ReadPosRankSum=-1.135e+00	GT:AD:DP:GQ:PL:SB	./.:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17	./.
+20	10096293	.	C	T,<NON_REF>	.	.	BaseQRankSum=4.66;DP=75;ExcessHet=3.01;MQRankSum=1.40;RAW_MQandDP=257261,75;ReadPosRankSum=-1.135e+00	GT:AD:DP:GQ:PL:SB	./.:37,38,0:75:99:1384,0,1258,1495,1372,2867:21,16,21,17	./.
 20	10096294	.	T	<NON_REF>	.	.	END=10096595	GT:DP:GQ:MIN_DP:PL	./.:68:99:57:0,120,1800	./.
-20	10096596	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.73;DP=87;ExcessHet=3.01;MQRankSum=0.612;RAW_MQ=300461.00;ReadPosRankSum=-1.700e-01	GT:AD:DP:GQ:PL:SB	./.:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24	./.
+20	10096596	.	C	T,<NON_REF>	.	.	BaseQRankSum=2.73;DP=87;ExcessHet=3.01;MQRankSum=0.612;RAW_MQandDP=300461,87;ReadPosRankSum=-1.700e-01	GT:AD:DP:GQ:PL:SB	./.:40,47,0:87:99:1591,0,1273,1711,1414,3125:19,21,23,24	./.
 20	10096597	.	T	<NON_REF>	.	.	END=10096767	GT:DP:GQ:MIN_DP:PL	./.:90:99:75:0,120,1800	./.
-20	10096768	.	A	C,<NON_REF>	.	.	BaseQRankSum=-2.764e+00;DP=91;ExcessHet=3.01;MQRankSum=-1.609e+00;RAW_MQ=319323.00;ReadPosRankSum=0.613	GT:AD:DP:GQ:PL:SB	./.:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25	./.
+20	10096768	.	A	C,<NON_REF>	.	.	BaseQRankSum=-2.764e+00;DP=91;ExcessHet=3.01;MQRankSum=-1.609e+00;RAW_MQandDP=319323,91;ReadPosRankSum=0.613	GT:AD:DP:GQ:PL:SB	./.:42,49,0:91:99:1711,0,1452,1838,1600,3437:25,17,24,25	./.
 20	10096769	.	A	<NON_REF>	.	.	END=10096898	GT:DP:GQ:MIN_DP:PL	./.:78:99:65:0,120,1800	./.
-20	10096899	.	G	T,<NON_REF>	.	.	BaseQRankSum=2.76;DP=79;ExcessHet=3.01;MQRankSum=-1.387e+00;RAW_MQ=279938.00;ReadPosRankSum=0.422	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28	./.
+20	10096899	.	G	T,<NON_REF>	.	.	BaseQRankSum=2.76;DP=79;ExcessHet=3.01;MQRankSum=-1.387e+00;RAW_MQandDP=279938,79;ReadPosRankSum=0.422	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:39,40,0:79:99:0|1:10096899_G_T:1643,0,1520,1764,1649,3413:19,20,12,28	./.
 20	10096900	.	G	<NON_REF>	.	.	END=10096904	GT:DP:GQ:MIN_DP:PL	./.:82:99:78:0,120,1800	./.
-20	10096905	.	TA	T,<NON_REF>	.	.	BaseQRankSum=-7.550e-01;DP=83;ExcessHet=3.01;MQRankSum=-1.677e+00;RAW_MQ=291579.00;ReadPosRankSum=0.461	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30	./.
+20	10096905	.	TA	T,<NON_REF>	.	.	BaseQRankSum=-7.550e-01;DP=83;ExcessHet=3.01;MQRankSum=-1.677e+00;RAW_MQandDP=291579,83;ReadPosRankSum=0.461	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30	./.
 20	10096906	.	A	*,<NON_REF>	.	.	DP=83	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:40,43,0:83:99:0|1:10096899_G_T:1638,0,1623,1768,1752,3520:20,20,13,30	./.
 20	10096907	.	A	<NON_REF>	.	.	END=10096932	GT:DP:GQ:MIN_DP:PL	./.:84:99:82:0,120,1800	./.
-20	10096933	.	G	C,<NON_REF>	.	.	BaseQRankSum=-1.914e+00;DP=85;ExcessHet=3.01;MQRankSum=-1.802e+00;RAW_MQ=298779.00;ReadPosRankSum=0.334	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28	./.
+20	10096933	.	G	C,<NON_REF>	.	.	BaseQRankSum=-1.914e+00;DP=85;ExcessHet=3.01;MQRankSum=-1.802e+00;RAW_MQandDP=298779,85;ReadPosRankSum=0.334	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:44,41,0:85:99:0|1:10096933_G_C:1540,0,1770,1684,1896,3580:28,16,13,28	./.
 20	10096934	.	T	<NON_REF>	.	.	END=10096957	GT:DP:GQ:MIN_DP:PL	./.:90:99:86:0,120,1800	./.
-20	10096958	.	G	A,<NON_REF>	.	.	BaseQRankSum=2.84;DP=92;ExcessHet=3.01;MQRankSum=-1.701e+00;RAW_MQ=323979.00;ReadPosRankSum=-1.833e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31	./.
+20	10096958	.	G	A,<NON_REF>	.	.	BaseQRankSum=2.84;DP=92;ExcessHet=3.01;MQRankSum=-1.701e+00;RAW_MQandDP=323979,92;ReadPosRankSum=-1.833e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:45,47,0:92:99:0|1:10096933_G_C:1795,0,1629,1929,1773,3702:27,18,16,31	./.
 20	10096959	.	G	<NON_REF>	.	.	END=10097074	GT:DP:GQ:MIN_DP:PL	./.:92:99:84:0,120,1800	./.
-20	10097075	.	T	G,<NON_REF>	.	.	BaseQRankSum=-2.533e+00;DP=92;ExcessHet=3.01;MQRankSum=-1.389e+00;RAW_MQ=315628.00;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	./.:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22	./.
+20	10097075	.	T	G,<NON_REF>	.	.	BaseQRankSum=-2.533e+00;DP=92;ExcessHet=3.01;MQRankSum=-1.389e+00;RAW_MQandDP=315628,92;ReadPosRankSum=0.082	GT:AD:DP:GQ:PL:SB	./.:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22	./.
 20	10097076	.	A	<NON_REF>	.	.	END=10097100	GT:DP:GQ:MIN_DP:PL	./.:91:99:77:0,120,1800	./.
-20	10097101	.	C	CTTT,CTTTT,<NON_REF>	.	.	BaseQRankSum=-1.134e+00;DP=76;ExcessHet=3.01;MQRankSum=-2.428e+00;RAW_MQ=252294.00;ReadPosRankSum=2.09	GT:AD:DP:GQ:PL:SB	./.:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15	./.
+20	10097101	.	C	CTTT,CTTTT,<NON_REF>	.	.	BaseQRankSum=-1.134e+00;DP=76;ExcessHet=3.01;MQRankSum=-2.428e+00;RAW_MQandDP=252294,76;ReadPosRankSum=2.09	GT:AD:DP:GQ:PL:SB	./.:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15	./.
 20	10097102	.	T	<NON_REF>	.	.	END=10097435	GT:DP:GQ:MIN_DP:PL	./.:70:99:60:0,120,1800	./.
-20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C,<NON_REF>	.	.	BaseQRankSum=1.82;DP=89;ExcessHet=3.01;MQRankSum=-6.464e+00;RAW_MQ=262143.00;ReadPosRankSum=-3.097e+00	GT:AD:DP:GQ:PL:SB	./.:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21	./.
-20	10097437	.	TTTTC	*,T,<NON_REF>	.	.	DP=76;ExcessHet=3.01;RAW_MQ=217330.00	GT:AD:DP:GQ:PL:SB	./.:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39	./.
+20	10097436	.	CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT	C,<NON_REF>	.	.	BaseQRankSum=1.82;DP=89;ExcessHet=3.01;MQRankSum=-6.464e+00;RAW_MQandDP=262143,89;ReadPosRankSum=-3.097e+00	GT:AD:DP:GQ:PL:SB	./.:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21	./.
+20	10097437	.	TTTTC	*,T,<NON_REF>	.	.	DP=76;ExcessHet=3.01;RAW_MQandDP=217330,76	GT:AD:DP:GQ:PL:SB	./.:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39	./.
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@@ -1386,18 +1468,18 @@
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@@ -1469,7 +1551,7 @@
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@@ -1486,7 +1568,7 @@
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@@ -1494,7 +1576,7 @@
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-20	10099034	.	C	A,<NON_REF>	.	.	BaseQRankSum=2.76;DP=28;ExcessHet=3.01;MQRankSum=-3.641e+00;RAW_MQ=79617.00;ReadPosRankSum=-1.850e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:13,5,9,1	./.
+20	10099034	.	C	A,<NON_REF>	.	.	BaseQRankSum=2.76;DP=28;ExcessHet=3.01;MQRankSum=-3.641e+00;RAW_MQandDP=79617,28;ReadPosRankSum=-1.850e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:18,10,0:28:99:0|1:10099029_T_C:363,0,768,420,798,1218:13,5,9,1	./.
 20	10099035	.	G	<NON_REF>	.	.	END=10099039	GT:DP:GQ:MIN_DP:PL	./.:29:60:26:0,60,900	./.
 20	10099040	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:26:51:26:0,51,765	./.
 20	10099041	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:27:54:27:0,54,810	./.
 20	10099042	.	T	<NON_REF>	.	.	END=10099043	GT:DP:GQ:MIN_DP:PL	./.:26:57:24:0,57,855	./.
-20	10099044	.	A	C,<NON_REF>	.	.	BaseQRankSum=-1.148e+00;DP=24;ExcessHet=3.01;MQRankSum=-4.418e+00;RAW_MQ=59851.00;ReadPosRankSum=-2.207e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2	./.
+20	10099044	.	A	C,<NON_REF>	.	.	BaseQRankSum=-1.148e+00;DP=24;ExcessHet=3.01;MQRankSum=-4.418e+00;RAW_MQandDP=59851,24;ReadPosRankSum=-2.207e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:15,9,0:24:99:0|1:10099029_T_C:363,0,768,420,798,1218:12,3,7,2	./.
 20	10099045	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:24:60:24:0,60,900	./.
-20	10099046	.	T	C,<NON_REF>	.	.	BaseQRankSum=-2.165e+00;DP=24;ExcessHet=3.01;MQRankSum=-4.418e+00;RAW_MQ=59851.00;ReadPosRankSum=-2.297e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2	./.
+20	10099046	.	T	C,<NON_REF>	.	.	BaseQRankSum=-2.165e+00;DP=24;ExcessHet=3.01;MQRankSum=-4.418e+00;RAW_MQandDP=59851,24;ReadPosRankSum=-2.297e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:15,9,0:24:99:0|1:10099029_T_C:333,0,603,378,630,1008:12,3,7,2	./.
 20	10099047	.	G	<NON_REF>	.	.	END=10099052	GT:DP:GQ:MIN_DP:PL	./.:24:57:23:0,57,855	./.
 20	10099053	.	G	<NON_REF>	.	.	END=10099054	GT:DP:GQ:MIN_DP:PL	./.:23:54:23:0,54,810	./.
-20	10099055	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.554e+00;DP=23;ExcessHet=3.01;MQRankSum=-4.316e+00;RAW_MQ=58555.00;ReadPosRankSum=-1.970e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2	./.
+20	10099055	.	T	C,<NON_REF>	.	.	BaseQRankSum=-1.554e+00;DP=23;ExcessHet=3.01;MQRankSum=-4.316e+00;RAW_MQandDP=58555,23;ReadPosRankSum=-1.970e+00	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:15,8,0:23:99:0|1:10099029_T_C:285,0,673,336,697,1033:11,4,6,2	./.
 20	10099056	.	T	<NON_REF>	.	.	END=10099061	GT:DP:GQ:MIN_DP:PL	./.:24:60:23:0,60,900	./.
 20	10099062	.	A	<NON_REF>	.	.	END=10099067	GT:DP:GQ:MIN_DP:PL	./.:25:72:24:0,72,921	./.
 20	10099068	.	G	<NON_REF>	.	.	END=10099072	GT:DP:GQ:MIN_DP:PL	./.:27:81:27:0,81,1042	./.
 20	10099073	.	T	<NON_REF>	.	.	END=10099077	GT:DP:GQ:MIN_DP:PL	./.:27:78:27:0,78,1170	./.
 20	10099078	.	G	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:28:81:28:0,81,1215	./.
-20	10099079	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.43;DP=29;ExcessHet=3.01;MQRankSum=-2.821e+00;RAW_MQ=78698.00;ReadPosRankSum=0.969	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2	./.
+20	10099079	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.43;DP=29;ExcessHet=3.01;MQRankSum=-2.821e+00;RAW_MQandDP=78698,29;ReadPosRankSum=0.969	GT:AD:DP:GQ:PGT:PID:PL:SB	./.:23,6,0:29:99:0|1:10099029_T_C:145,0,886,217,904,1120:11,12,4,2	./.
 20	10099080	.	G	<NON_REF>	.	.	END=10099089	GT:DP:GQ:MIN_DP:PL	./.:30:81:29:0,81,1215	./.
 20	10099090	.	A	<NON_REF>	.	.	END=10099095	GT:DP:GQ:MIN_DP:PL	./.:34:90:31:0,90,1350	./.
 20	10099096	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:35:74:35:0,74,1310	./.
@@ -1529,13 +1611,13 @@
 20	10099101	.	G	<NON_REF>	.	.	END=10099105	GT:DP:GQ:MIN_DP:PL	./.:37:99:36:0,99,1485	./.
 20	10099106	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:36:96:36:0,96,1440	./.
 20	10099107	.	T	<NON_REF>	.	.	END=10099110	GT:DP:GQ:MIN_DP:PL	./.:41:99:39:0,99,1485	./.
-20	10099111	.	T	TTTTGTTTG,<NON_REF>	.	.	BaseQRankSum=-1.207e+00;DP=42;ExcessHet=3.01;MQRankSum=-4.071e+00;RAW_MQ=109737.00;ReadPosRankSum=-2.730e-01	GT:AD:DP:GQ:PL:SB	./.:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6	./.
+20	10099111	.	T	TTTTGTTTG,<NON_REF>	.	.	BaseQRankSum=-1.207e+00;DP=42;ExcessHet=3.01;MQRankSum=-4.071e+00;RAW_MQandDP=109737,42;ReadPosRankSum=-2.730e-01	GT:AD:DP:GQ:PL:SB	./.:22,13,0:35:99:694,0,802,763,859,1622:13,9,7,6	./.
 20	10099112	.	T	<NON_REF>	.	.	END=10099139	GT:DP:GQ:MIN_DP:PL	./.:57:99:49:0,114,1710	./.
-20	10099140	.	G	T,<NON_REF>	.	.	BaseQRankSum=-1.140e-01;DP=62;ExcessHet=3.01;MQRankSum=-2.469e+00;RAW_MQ=192512.00;ReadPosRankSum=0.338	GT:AD:DP:GQ:PL:SB	./.:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10	./.
+20	10099140	.	G	T,<NON_REF>	.	.	BaseQRankSum=-1.140e-01;DP=62;ExcessHet=3.01;MQRankSum=-2.469e+00;RAW_MQandDP=192512,62;ReadPosRankSum=0.338	GT:AD:DP:GQ:PL:SB	./.:30,32,0:62:99:1034,0,931,1122,1028,2150:18,12,22,10	./.
 20	10099141	.	G	<NON_REF>	.	.	END=10099189	GT:DP:GQ:MIN_DP:PL	./.:67:99:64:0,120,1800	./.
-20	10099190	.	G	T,<NON_REF>	.	.	BaseQRankSum=-3.400e-02;DP=65;ExcessHet=3.01;MQRankSum=-1.711e+00;RAW_MQ=215351.00;ReadPosRankSum=-1.260e+00	GT:AD:DP:GQ:PL:SB	./.:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11	./.
+20	10099190	.	G	T,<NON_REF>	.	.	BaseQRankSum=-3.400e-02;DP=65;ExcessHet=3.01;MQRankSum=-1.711e+00;RAW_MQandDP=215351,65;ReadPosRankSum=-1.260e+00	GT:AD:DP:GQ:PL:SB	./.:33,32,0:65:99:1063,0,1154,1162,1251,2413:21,12,21,11	./.
 20	10099191	.	C	<NON_REF>	.	.	END=10099219	GT:DP:GQ:MIN_DP:PL	./.:58:99:46:0,111,1665	./.
-20	10099220	.	A	G,<NON_REF>	.	.	BaseQRankSum=-1.664e+00;DP=45;ExcessHet=3.01;MQRankSum=-2.596e+00;RAW_MQ=149477.00;ReadPosRankSum=0.629	GT:AD:DP:GQ:PL:SB	./.:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9	./.
+20	10099220	.	A	G,<NON_REF>	.	.	BaseQRankSum=-1.664e+00;DP=45;ExcessHet=3.01;MQRankSum=-2.596e+00;RAW_MQandDP=149477,45;ReadPosRankSum=0.629	GT:AD:DP:GQ:PL:SB	./.:25,20,0:45:99:606,0,873,681,933,1614:15,10,11,9	./.
 20	10099221	.	T	<NON_REF>	.	.	END=10099229	GT:DP:GQ:MIN_DP:PL	./.:44:99:42:0,102,1530	./.
 20	10099230	.	T	<NON_REF>	.	.	END=10099233	GT:DP:GQ:MIN_DP:PL	./.:41:90:41:0,90,1350	./.
 20	10099234	.	T	<NON_REF>	.	.	END=10099235	GT:DP:GQ:MIN_DP:PL	./.:44:87:44:0,87,1305	./.
@@ -1543,16 +1625,16 @@
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 20	10099247	.	C	<NON_REF>	.	.	END=10099248	GT:DP:GQ:MIN_DP:PL	./.:37:93:36:0,93,1395	./.
 20	10099249	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:36:87:36:0,87,1305	./.
-20	10099250	.	G	A,<NON_REF>	.	.	BaseQRankSum=3.17;DP=37;ExcessHet=3.01;MQRankSum=-2.272e+00;RAW_MQ=119006.00;ReadPosRankSum=0.583	GT:AD:DP:GQ:PL:SB	./.:16,21,0:37:99:728,0,424,776,487,1263:12,4,11,10	./.
+20	10099250	.	G	A,<NON_REF>	.	.	BaseQRankSum=3.17;DP=37;ExcessHet=3.01;MQRankSum=-2.272e+00;RAW_MQandDP=119006,37;ReadPosRankSum=0.583	GT:AD:DP:GQ:PL:SB	./.:16,21,0:37:99:728,0,424,776,487,1263:12,4,11,10	./.
 20	10099251	.	A	<NON_REF>	.	.	END=10099269	GT:DP:GQ:MIN_DP:PL	./.:30:81:28:0,81,1132	./.
-20	10099270	.	A	C,<NON_REF>	.	.	BaseQRankSum=-2.866e+00;DP=30;ExcessHet=3.01;MQRankSum=-2.691e+00;RAW_MQ=98268.00;ReadPosRankSum=-1.380e-01	GT:AD:DP:GQ:PL:SB	./.:27,3,0:30:60:0,60,1084,81,1092,1113:19,8,0,3	./.
+20	10099270	.	A	C,<NON_REF>	.	.	BaseQRankSum=-2.866e+00;DP=30;ExcessHet=3.01;MQRankSum=-2.691e+00;RAW_MQandDP=98268,30;ReadPosRankSum=-1.380e-01	GT:AD:DP:GQ:PL:SB	./.:27,3,0:30:60:0,60,1084,81,1092,1113:19,8,0,3	./.
 20	10099271	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:31:84:31:0,84,1260	./.
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-20	10099535	.	G	A,<NON_REF>	.	.	BaseQRankSum=5.03;DP=65;ExcessHet=3.01;MQRankSum=-1.418e+00;RAW_MQ=226251.00;ReadPosRankSum=-7.770e-01	GT:AD:DP:GQ:PL:SB	./.:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17	./.
+20	10099535	.	G	A,<NON_REF>	.	.	BaseQRankSum=5.03;DP=65;ExcessHet=3.01;MQRankSum=-1.418e+00;RAW_MQandDP=226251,65;ReadPosRankSum=-7.770e-01	GT:AD:DP:GQ:PL:SB	./.:26,39,0:65:99:1364,0,686,1442,803,2245:17,9,22,17	./.
 20	10099536	.	T	<NON_REF>	.	.	END=10099564	GT:DP:GQ:MIN_DP:PL	./.:67:99:63:0,120,1800	./.
-20	10099565	.	C	T,<NON_REF>	.	.	BaseQRankSum=4.59;DP=69;ExcessHet=3.01;MQRankSum=-1.266e+00;RAW_MQ=243410.00;ReadPosRankSum=1.23	GT:AD:DP:GQ:PL:SB	./.:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17	./.
+20	10099565	.	C	T,<NON_REF>	.	.	BaseQRankSum=4.60;DP=69;ExcessHet=3.01;MQRankSum=-1.266e+00;RAW_MQandDP=243410,69;ReadPosRankSum=1.23	GT:AD:DP:GQ:PL:SB	./.:31,38,0:69:99:1375,0,994,1468,1108,2576:23,8,21,17	./.
 20	10099566	.	T	<NON_REF>	.	.	END=10099754	GT:DP:GQ:MIN_DP:PL	./.:77:99:66:0,120,1800	./.
-20	10099755	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.55;DP=65;ExcessHet=3.01;MQRankSum=-2.200e-02;RAW_MQ=229010.00;ReadPosRankSum=-2.300e-01	GT:AD:DP:GQ:PL:SB	./.:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15	./.
+20	10099755	.	C	T,<NON_REF>	.	.	BaseQRankSum=1.55;DP=65;ExcessHet=3.01;MQRankSum=-2.200e-02;RAW_MQandDP=229010,65;ReadPosRankSum=-2.300e-01	GT:AD:DP:GQ:PL:SB	./.:33,32,0:65:99:1127,0,1148,1226,1245,2470:20,13,17,15	./.
 20	10099756	.	C	<NON_REF>	.	.	END=10099831	GT:DP:GQ:MIN_DP:PL	./.:63:99:58:0,120,1800	./.
-20	10099832	.	A	G,<NON_REF>	.	.	BaseQRankSum=-4.563e+00;DP=72;ExcessHet=3.01;MQRankSum=0.869;RAW_MQ=250276.00;ReadPosRankSum=-1.023e+00	GT:AD:DP:GQ:PL:SB	./.:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19	./.
+20	10099832	.	A	G,<NON_REF>	.	.	BaseQRankSum=-4.563e+00;DP=72;ExcessHet=3.01;MQRankSum=0.869;RAW_MQandDP=250276,72;ReadPosRankSum=-1.023e+00	GT:AD:DP:GQ:PL:SB	./.:39,33,0:72:99:1102,0,1430,1220,1530,2749:22,17,14,19	./.
 20	10099833	.	T	<NON_REF>	.	.	END=10100000	GT:DP:GQ:MIN_DP:PL	./.:85:99:73:0,120,1800	./.
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf.idx
index f7516a705a3e7d5968291faed25b365982e4a2e4..77aa52fad85d9611d85c54c6b8841a3ac7b97656 100644
GIT binary patch
literal 42427
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literal 40774
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf
deleted file mode 100644
index d0f8b7155ab..00000000000
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf
+++ /dev/null
@@ -1,11613 +0,0 @@
-##fileformat=VCFv4.2
-##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
-##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=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
-##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##FORMAT=<ID=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 /var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsdb-tests-2160631194140750294/workspace --variant /Users/gauthier/workspaces/gatk/src/test/resources/org/broadinstitute/hellbender/tools//haplotypecaller/expected.testGVCFMode.gatk4.g.vcf --variant src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/YRIoffspring.chr20snippet.g.vcf --batch-size 0 --reader-threads 1 --intervals 20:1-11000000 --verbosity ERROR  --genomicsdb-segment-size 1048576 --genomicsdb-vcf-buffer-size 16384 --overwrite-existing-genomicsdb-workspace false --consolidate false --validate-sample-name-map false --max-num-intervals-to-import-in-parallel 1 --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 --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 --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=Unavailable,Date="September 18, 2018 1:44:33 PM EDT">
-##GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants  --output src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf --variant gendb:///var/folders/v5/gbkn5lv95c51kj3xpx5pzncscnxf_m/T/genomicsdb-tests-2160631194140750294/workspace --reference /Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta  --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 --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 --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=4.0.8.1-42-g21f16d5-SNAPSHOT,Date="September 18, 2018 1:45:39 PM EDT">
-##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)
-##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)
-##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)
-##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)
-##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)
-##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)
-##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)
-##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)
-##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)
-##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)
-##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)
-##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)
-##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)
-##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)
-##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)
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-##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)
-##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)
-##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)
-##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)
-##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)
-##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)
-##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)
-##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)
-##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)
-##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)
-##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)
-##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)
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-##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)
-##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)
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-##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)
-##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)
-##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)
-##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)
-##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)
-##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)
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-##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)
-##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)
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-##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)
-##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)
-##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)
-##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)
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-##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)
-##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)
-##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)
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-##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)
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-##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)
-##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)
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-##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)
-##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)
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-##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)
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-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
-##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
-##INFO=<ID=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=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##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">
-##contig=<ID=20,length=63025520,assembly=human_g1k_v37.20.21.fasta>
-##contig=<ID=21,length=48129895,assembly=human_g1k_v37.20.21.fasta>
-##reference=file:///Users/gauthier/workspaces/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta
-##source=GenomicsDBImport
-##source=SelectVariants
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
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-20	10000384	.	A	<NON_REF>	.	.	END=10000386	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:34:86:34:0,86,1023
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-20	10000390	.	T	<NON_REF>	.	.	END=10000391	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:32:78:32:0,78,1170
-20	10000392	.	A	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:32:63:32:0,63,884
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-20	10000401	.	T	<NON_REF>	.	.	END=10000402	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:32:80:31:0,80,993
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-20	10000404	.	T	<NON_REF>	.	.	END=10000405	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:33:86:33:0,86,1022
-20	10000406	.	T	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:34:90:34:0,90,1350
-20	10000407	.	C	<NON_REF>	.	.	.	GT:DP:GQ:MIN_DP:PL	./.:79:99:55:0,120,1800	./.:32:78:32:0,78,980
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diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenomicsDBImport/newMQcalc.combined.g.vcf.idx
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