##fileformat=VCFv4.1
##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/projects/bsi/bictools/apps/alignment/GenomeAnalysisTK/1.6-5-g557da77/Hossain.Asif_mayo.edu.key read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=/data2/bsi/RandD/sampleData/Genome_GPS/sb/exome/110815_SN316_0162_AD07MMACXX/variants//s_tumor/s_tumor.variants.chr22.raw.vcf), (RodBinding name=variant2 source=/data2/bsi/RandD/sampleData/Genome_GPS/sb/exome/110815_SN316_0162_AD07MMACXX/variants//s_tumor/s_tumor.variants.chr21.raw.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=variant2,variant printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
##FORMAT=<ID=AD,Number=.,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=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=ED,Number=1,Type=Integer,Description="Number of blat hits to reference genome, not counting self-hit">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##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=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##INFO=<ID=rsID,Number=.,Type=String,Description="Semi-colon separated list of unique identifiers.  If this is a dbSNP variant, the rs number(s) should be used.  (VCF field)">
##INFO=<ID=dbSNP.build,Number=.,Type=Integer,Description="First dbSNP Build for RS">
##INFO=<ID=dbSNP.SuspectRegion,Number=.,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
##INFO=<ID=dbSNP.SNP_Allele_Origin,Number=.,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
##INFO=<ID=dbSNP.ClinicalSig,Number=.,Type=String,Description="Variant Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other">
##INFO=<ID=dbSNP.DiseaseVariant,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=COSMIC.Mutation_ID,Number=.,Type=String,Description="This id is used to identify a mutation within the COSMIC database and is assigned as the mutation is curated">
##INFO=<ID=COSMIC.Mutation_CDS,Number=.,Type=String,Description="The change that has occurred in the nucleotide sequence as a result of the mutation">
##INFO=<ID=COSMIC.Mutation_AA,Number=.,Type=String,Description="The change that has occurred in the peptide sequence as a result of the mutation">
##INFO=<ID=COSMIC.strand,Number=.,Type=String,Description="Strand based on GRCh37 genome build">
##INFO=<ID=1000Genomes.ASN_AF,Number=.,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
##INFO=<ID=1000Genomes.AMR_AF,Number=.,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
##INFO=<ID=1000Genomes.AFR_AF,Number=.,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
##INFO=<ID=1000Genomes.EUR_AF,Number=.,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
##INFO=<ID=BGI200_Danish_MAF,Number=.,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=ESP6500.EUR_MAF,Number=.,Type=Float,Description="European American Minor Allele Frequency (in percent)">
##INFO=<ID=ESP6500.AFR_MAF,Number=.,Type=Float,Description="African American Minor Allele Frequency (in percent)">
##INFO=<ID=HapMap.CEU_MAF,Number=.,Type=Float,Description="Other allele frequency(Utah residents with Northern and Western European ancestry from the CEPH collection)">
##INFO=<ID=HapMap.YRI_MAF,Number=.,Type=Float,Description="Other Allele Frequency(Han Chinese in Beijing China)">
##INFO=<ID=HapMap.JPT_MAF,Number=.,Type=Float,Description="Other Allele Frequency(Japanese in Tokyo Japan)">
##INFO=<ID=HapMap.CHB_MAF,Number=.,Type=Float,Description="Other Allele Frequency(Yoruban in Ibadan  Nigeria)">
##INFO=<ID=Entrez.GeneID,Number=.,Type=String,Description="Entrez Gene ID">
##INFO=<ID=Gene_Symbol,Number=.,Type=String,Description="Official Gene Symbol provided by HGNC">
##INFO=<ID=Approved_Gene_Name,Number=.,Type=String,Description="The official gene name that has been approved by the HGNC and is publicly available">
##INFO=<ID=Ensembl_Gene_ID,Number=.,Type=String,Description="This column contains a manually curated Ensembl Gene ID">
##INFO=<ID=OMIM.ID,Number=.,Type=Integer,Description="Phenotype MIM Number">
##INFO=<ID=OMIM.Disease,Number=.,Type=String,Description="Phenotypes observed">
##INFO=<ID=miRBASE.ID,Number=.,Type=String,Description="Semi-colon separated list of unique identifiers.  If this is a dbSNP variant  the rs number(s) should be used.  (VCF field)">
##INFO=<ID=UCSC.BlacklistedRegion,Number=.,Type=Integer,Description="Score from 0-1000(Indicates confidence of the annotation.Higher the score higher the confidence)">
##INFO=<ID=UCSC.conservation,Number=.,Type=Integer,Description="Score from 0-1000 (conservation scores based on a phylo-HMM)">
##INFO=<ID=UCSC.regulation,Number=.,Type=String,Description="unique ID to identify this regulatory region">
##INFO=<ID=UCSC.tfbs,Number=.,Type=Integer,Description="Score from 0-1000">
##INFO=<ID=UCSC.tss,Number=.,Type=Integer,Description="Score">
##INFO=<ID=UCSC.enhancer,Number=.,Type=Integer,Description="Score from 0-1000(Elements that tested positive are assigned a score of 900 and where as negative are assigned score of 200)">
##INFO=<ID=UCSC.Alignability/Uniqueness,Number=.,Type=Integer,Description="Score from 0-1000(Indicates confidence of the annotation.Higher the score higher the confidence)">
##INFO=<ID=UCSC.Repeat_Region,Number=.,Type=Integer,Description="Smith Waterman alignment score">
##INFO=<ID=VEP.Allele,Number=.,Type=String,Description="The variant allele used to calculate the consequence.">
##INFO=<ID=VEP.Gene,Number=.,Type=String,Description="Ensembl stable ID of affected gene.">
##INFO=<ID=VEP.Feature,Number=.,Type=String,Description="Ensembl stable ID of feature.">
##INFO=<ID=VEP.Feature_type,Number=.,Type=String,Description="Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature.">
##INFO=<ID=VEP.Consequence,Number=.,Type=String,Description="Consequence type, a term defined by the Sequence Ontology (SO), of this variation.">
##INFO=<ID=VEP.cDNA_position,Number=.,Type=String,Description="Relative position of base pair in cDNA sequence.">
##INFO=<ID=VEP.CDS_position,Number=.,Type=String,Description="Relative position of base pair in coding sequence.">
##INFO=<ID=VEP.Protein_position,Number=.,Type=String,Description="Relative position of amino acid in protein.">
##INFO=<ID=VEP.Amino_acids,Number=.,Type=String,Description="Only given if the variation affects the protein-coding sequence.">
##INFO=<ID=VEP.Codons,Number=.,Type=String,Description="The alternative codons with the variant base in upper case.">
##INFO=<ID=VEP.HGNC,Number=.,Type=String,Description="The HGNC gene identifier.">
##INFO=<ID=SIFT.TERM,Number=.,Type=String,Description="The SIFT prediction.">
##INFO=<ID=SIFT.Score,Number=.,Type=Float,Description="The SIFT score.">
##INFO=<ID=PolyPhen.TERM,Number=.,Type=String,Description="The PolyPhen prediction.">
##INFO=<ID=PolyPhen.Score,Number=.,Type=Float,Description="The PolyPhen score.">
##INFO=<ID=UniprotID,Number=.,Type=String,Description="The UniProt identifier provided by the EBI.">
##INFO=<ID=SNPEFF.Effect,Number=.,Type=String,Description="Effect of this variant. {INTERGENIC, UPSTREAM, UTR_5_PRIME, UTR_5_DELETED, START_GAINED, SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, SYNONYMOUS_START, CDS, GENE, TRANSCRIPT, EXON, EXON_DELETED, NON_SYNONYMOUS_CODING, SYNONYMOUS_CODING, FRAME_SHIFT, CODON_CHANGE, CODON_INSERTION, CODON_CHANGE_PLUS_CODON_INSERTION, CODON_DELETION, CODON_CHANGE_PLUS_CODON_DELETION, STOP_GAINED, SYNONYMOUS_STOP, STOP_LOST, INTRON, UTR_3_PRIME, UTR_3_DELETED, DOWNSTREAM, INTRON_CONSERVED, INTERGENIC_CONSERVED, INTRAGENIC, RARE_AMINO_ACID, NON_SYNONYMOUS_START}">
##INFO=<ID=SNPEFF.Effect_impact,Number=.,Type=String,Description="Effects are categorized by 'impact' categories to help users find more significant variants. {HIGH, MODERATE, LOW, MODIFIER}">
##INFO=<ID=SNPEFF.Functional_class,Number=.,Type=String,Description="Functional class. {NONE, SILENT, MISSENSE, NONSENSE}">
##INFO=<ID=SNPEFF.Codon_change,Number=.,Type=String,Description="Codon change: old_codon/new_codon OR distance to transcript (in case of upstream / downstream).">
##INFO=<ID=SNPEFF.Amino_acid_change,Number=.,Type=String,Description="Amino acid change: old_AA AA_position/new_AA (e.g. 'E30K').">
##INFO=<ID=SNPEFF.Gene_name,Number=.,Type=String,Description="Gene name">
##INFO=<ID=SNPEFF.Gene_bioType,Number=.,Type=String,Description="Transcript bioType, if available.">
##INFO=<ID=SNPEFF.Coding,Number=.,Type=String,Description="This field is 'CODING' if any transcript of the gene is marked as protein coding. {CODING, NON_CODING}">
##INFO=<ID=SNPEFF.Transcript,Number=.,Type=String,Description="Transcript ID (usually ENSEMBL IDs).">
##INFO=<ID=SNPEFF.Exon,Number=.,Type=String,Description="Exon rank or Intron rank (e.g. '1' for the first exon, '2' for the second exon, etc.).">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/data2/bsi/RandD/sampleData/Genome_GPS//sb/exome/110815_SN316_0162_AD07MMACXX/variants/s_tumor/s_tumor.chr21-sorted.bam] read_buffer_size=null phone_home=NO_ET gatk_key=/projects/bsi/bictools/apps/alignment/GenomeAnalysisTK/1.6-5-g557da77/Hossain.Asif_mayo.edu.key read_filter=[] intervals=[chr21] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=2 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chrGL000191.1,length=106433>
##contig=<ID=chrGL000192.1,length=547496>
##contig=<ID=chrGL000193.1,length=189789>
##contig=<ID=chrGL000194.1,length=191469>
##contig=<ID=chrGL000195.1,length=182896>
##contig=<ID=chrGL000196.1,length=38914>
##contig=<ID=chrGL000197.1,length=37175>
##contig=<ID=chrGL000198.1,length=90085>
##contig=<ID=chrGL000199.1,length=169874>
##contig=<ID=chrGL000200.1,length=187035>
##contig=<ID=chrGL000201.1,length=36148>
##contig=<ID=chrGL000202.1,length=40103>
##contig=<ID=chrGL000203.1,length=37498>
##contig=<ID=chrGL000204.1,length=81310>
##contig=<ID=chrGL000205.1,length=174588>
##contig=<ID=chrGL000206.1,length=41001>
##contig=<ID=chrGL000207.1,length=4262>
##contig=<ID=chrGL000208.1,length=92689>
##contig=<ID=chrGL000209.1,length=159169>
##contig=<ID=chrGL000210.1,length=27682>
##contig=<ID=chrGL000211.1,length=166566>
##contig=<ID=chrGL000212.1,length=186858>
##contig=<ID=chrGL000213.1,length=164239>
##contig=<ID=chrGL000214.1,length=137718>
##contig=<ID=chrGL000215.1,length=172545>
##contig=<ID=chrGL000216.1,length=172294>
##contig=<ID=chrGL000217.1,length=172149>
##contig=<ID=chrGL000218.1,length=161147>
##contig=<ID=chrGL000219.1,length=179198>
##contig=<ID=chrGL000220.1,length=161802>
##contig=<ID=chrGL000221.1,length=155397>
##contig=<ID=chrGL000222.1,length=186861>
##contig=<ID=chrGL000223.1,length=180455>
##contig=<ID=chrGL000224.1,length=179693>
##contig=<ID=chrGL000225.1,length=211173>
##contig=<ID=chrGL000226.1,length=15008>
##contig=<ID=chrGL000227.1,length=128374>
##contig=<ID=chrGL000228.1,length=129120>
##contig=<ID=chrGL000229.1,length=19913>
##contig=<ID=chrGL000230.1,length=43691>
##contig=<ID=chrGL000231.1,length=27386>
##contig=<ID=chrGL000232.1,length=40652>
##contig=<ID=chrGL000233.1,length=45941>
##contig=<ID=chrGL000234.1,length=40531>
##contig=<ID=chrGL000235.1,length=34474>
##contig=<ID=chrGL000236.1,length=41934>
##contig=<ID=chrGL000237.1,length=45867>
##contig=<ID=chrGL000238.1,length=39939>
##contig=<ID=chrGL000239.1,length=33824>
##contig=<ID=chrGL000240.1,length=41933>
##contig=<ID=chrGL000241.1,length=42152>
##contig=<ID=chrGL000242.1,length=43523>
##contig=<ID=chrGL000243.1,length=43341>
##contig=<ID=chrGL000244.1,length=39929>
##contig=<ID=chrGL000245.1,length=36651>
##contig=<ID=chrGL000246.1,length=38154>
##contig=<ID=chrGL000247.1,length=36422>
##contig=<ID=chrGL000248.1,length=39786>
##contig=<ID=chrGL000249.1,length=38502>
##contig=<ID=chrM,length=16569>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##reference=file:///data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s_tumor
chr21	9411327	.	C	G	884.22	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=2.004;DP=47;Dels=0.00;ED=5;FS=9.784;HRun=1;HaplotypeScore=0.0000;MQ=138.53;MQ0=0;MQRankSum=1.162;QD=18.81;ReadPosRankSum=0.144;SB=-78.71;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs75025155;dbSNP.build=131;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:17,30:47:99:914,0,432
chr21	9411410	.	C	T	1060.02	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-0.055;DP=71;Dels=0.00;ED=5;FS=0.000;HRun=1;HaplotypeScore=0.9469;MQ=138.95;MQ0=3;MQRankSum=-0.055;QD=14.93;ReadPosRankSum=-2.611;SB=-311.23;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs78200054;dbSNP.build=131;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:33,38:71:99:1090,0,817
chr21	9411500	.	G	T	1531.16	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-6.149;DP=101;Dels=0.00;ED=5;FS=2.765;HRun=0;HaplotypeScore=0.0000;MQ=136.91;MQ0=2;MQRankSum=-0.467;QD=15.16;ReadPosRankSum=0.579;SB=-653.01;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs71235073;dbSNP.build=130;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:46,55:101:99:1561,0,1280
chr21	9411602	.	T	C	977	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-5.229;DP=112;Dels=0.00;ED=5;FS=0.000;HRun=0;HaplotypeScore=2.4131;MQ=107.17;MQ0=1;MQRankSum=2.874;QD=8.72;ReadPosRankSum=-0.506;SB=-328.91;set=variant2;SNPEFF.Functional_class=NONE;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:71,40:112:99:1007,0,1960
chr21	9411609	.	G	T	1095.35	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=1.076;DP=120;Dels=0.00;ED=5;FS=0.742;HRun=1;HaplotypeScore=4.3857;MQ=108.23;MQ0=1;MQRankSum=2.994;QD=9.13;ReadPosRankSum=-0.478;SB=-466.11;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs76676778;dbSNP.build=131;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:79,41:120:99:1125,0,2184
chr21	9411635	.	C	T	243.31	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=4.264;DP=124;Dels=0.00;ED=5;FS=28.451;HRun=1;HaplotypeScore=19.6910;MQ=111.47;MQ0=1;MQRankSum=-5.653;QD=1.96;ReadPosRankSum=4.258;SB=-0.01;set=variant2;SNPEFF.Functional_class=NONE;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:99,25:124:99:273,0,3146
chr21	9411645	.	A	G	1103.37	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-6.787;DP=121;Dels=0.00;ED=5;FS=3.568;HRun=0;HaplotypeScore=18.7077;MQ=116.17;MQ0=2;MQRankSum=1.748;QD=9.12;ReadPosRankSum=-2.226;SB=-452.55;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs71235074;dbSNP.build=130;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC	GT:AD:DP:GQ:PL	0/1:72,49:121:99:1133,0,1876
