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Copy pathpatient2_t.mutect2.pass.chr20-22.vcf
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patient2_t.mutect2.pass.chr20-22.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=clustered_read_position,Description="Evidence for somatic variant clusters near the ends of reads">
##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor">
##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal">
##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals">
##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_artifact,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=t_lod_fstar,Description="Tumor does not meet likelihood threshold">
##FILTER=<ID=triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele fraction of the event in the tumor">
##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the alternate allele">
##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the alternate allele">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description="Fraction of alt reads indicating OxoG error">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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=QSS,Number=A,Type=Integer,Description="Sum of base quality scores for each allele">
##FORMAT=<ID=REF_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the reference allele">
##FORMAT=<ID=REF_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the reference allele">
##GATKCommandLine.MuTect2=<ID=MuTect2,Version=3.7-0-gcfedb67,Date="Tue Jun 06 03:03:40 CEST 2017",Epoch=1496711020882,CommandLineOptions="analysis_type=MuTect2 input_file=[patient2_t.final.bam, patient2_n.final.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/projects/pr_46630/data/references/human_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=12 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false cosmic=[(RodBinding name=cosmic source=/home/projects/pr_46630/data/references/human_GRCh38/cosmic/CosmicCodingMuts_chr_sorted.vcf)] normal_panel=[] dbsnp=(RodBinding name=dbsnp source=/home/projects/pr_46630/data/references/all/All_20160527_chr.vcf) m2debug=false artifact_detection_mode=false initial_tumor_lod=4.0 initial_normal_lod=0.5 tumor_lod=6.3 normal_lod=2.2 dbsnp_normal_lod=5.5 max_alt_alleles_in_normal_count=1 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 power_constant_qscore=30 strand_artifact_lod=2.0 strand_artifact_power_threshold=0.9 enable_strand_artifact_filter=false enable_clustered_read_position_filter=false pir_median_threshold=10.0 pir_mad_threshold=3.0 debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false debug_read_name=null MQ_filtering_level=20 comp=[] annotation=[DepthPerAlleleBySample, BaseQualitySumPerAlleleBySample, TandemRepeatAnnotator, OxoGReadCounts] excludeAnnotation=[SpanningDeletions] out=/home/projects/pr_46630/data/NGScourse/patient2_t.mutect2.vcf dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 keepRG=null min_base_quality_score=10 errorCorrectReads=false captureAssemblyFailureBAM=false dontUseSoftClippedBases=false justDetermineActiveRegions=false doNotRunPhysicalPhasing=false maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=ECNT,Number=1,Type=String,Description="Number of events in this haplotype">
##INFO=<ID=HCNT,Number=1,Type=String,Description="Number of haplotypes that support this variant">
##INFO=<ID=MAX_ED,Number=1,Type=Integer,Description="Maximum distance between events in this active region">
##INFO=<ID=MIN_ED,Number=1,Type=Integer,Description="Minimum distance between events in this active region">
##INFO=<ID=NLOD,Number=1,Type=String,Description="Normal LOD score">
##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=TLOD,Number=1,Type=String,Description="Tumor LOD score">
##SAMPLE=<ID=NORMAL,SampleName=TCRBOA2-N-WEX,File=/home/projects/pr_46630/data/NGScourse/patient2_n.final.bam>
##SAMPLE=<ID=TUMOR,SampleName=TCRBOA2-T-WEX,File=/home/projects/pr_46630/data/NGScourse/patient2_t.final.bam>
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chrM,length=16569>
##reference=file:///home/projects/pr_46630/data/references/human_GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fa
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL
chr20 28581022 . C T . PASS . GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:8,3:0.273:1:2:0.667:294,101:5:3 0/0:9,0:0.00:0:0:.:322,0:3:6
chr20 45969597 rs200638247 A C . PASS . GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:14,6:0.300:3:3:0.500:473,129:6:8 0/0:19,1:0.056:0:1:1.00:594,5:4:15
chr21 10453957 rs2698583 G A . PASS . GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:13,3:0.188:2:1:0.667:363,107:9:4 0/0:20,0:0.00:0:0:.:551,0:8:12
chr22 15631892 rs2259866 G A . PASS . GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:PGT:PID:QSS:REF_F1R2:REF_F2R1 0/1:80,3:0.041:1:2:0.333:0|1:15631892_G_A:2310,103:37:43 0/0:70,0:0.016:0:0:.:0|1:15631892_G_A:2064,0:29:41
chr22 20977711 rs765401131 G A . PASS . GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:54,4:0.060:2:2:0.500:1566,137:27:27 0/0:54,0:0.00:0:0:.:1602,0:25:29