##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">
##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	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	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	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	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	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	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	GT:AD:DP:GQ:PL	0/1:72,49:121:99:1133,0,1876
