Mercurial > repos > devteam > vcftools_consensus
comparison test-data/sample1.vcf @ 0:b5684d716c68 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus commit caca2f9bbd012d710d7c9d16df5c4eb9237cd33c-dirty
| author | devteam |
|---|---|
| date | Fri, 04 Nov 2016 15:07:44 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:b5684d716c68 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> | |
| 3 ##FILTER=<ID=LowQual,Description="Low quality"> | |
| 4 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| 5 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | |
| 6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| 7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 8 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> | |
| 9 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | |
| 10 ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> | |
| 11 ##GATKCommandLine=<ID=HaplotypeCaller,Version=3.3-0-g37228af,Date="Sun Jun 07 11:35:17 SAST 2015",Epoch=1433669717749,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[./R_2997_878#L6-_.R.bam.sorted_dedup.bam_realigned.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=reference_H37Rv.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 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 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 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=4 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=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bamWriterType=CALLED_HAPLOTYPES disableOptimizations=false dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=1 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=true sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false doNotRunPhysicalPhasing=true pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=1000 minReadsPerAlignmentStart=5 activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> | |
| 12 ##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) | |
| 13 ##GVCFBlock=minGQ=1(inclusive),maxGQ=2(exclusive) | |
| 14 ##GVCFBlock=minGQ=10(inclusive),maxGQ=11(exclusive) | |
| 15 ##GVCFBlock=minGQ=11(inclusive),maxGQ=12(exclusive) | |
| 16 ##GVCFBlock=minGQ=12(inclusive),maxGQ=13(exclusive) | |
| 17 ##GVCFBlock=minGQ=13(inclusive),maxGQ=14(exclusive) | |
| 18 ##GVCFBlock=minGQ=14(inclusive),maxGQ=15(exclusive) | |
| 19 ##GVCFBlock=minGQ=15(inclusive),maxGQ=16(exclusive) | |
| 20 ##GVCFBlock=minGQ=16(inclusive),maxGQ=17(exclusive) | |
| 21 ##GVCFBlock=minGQ=17(inclusive),maxGQ=18(exclusive) | |
| 22 ##GVCFBlock=minGQ=18(inclusive),maxGQ=19(exclusive) | |
| 23 ##GVCFBlock=minGQ=19(inclusive),maxGQ=20(exclusive) | |
| 24 ##GVCFBlock=minGQ=2(inclusive),maxGQ=3(exclusive) | |
| 25 ##GVCFBlock=minGQ=20(inclusive),maxGQ=21(exclusive) | |
| 26 ##GVCFBlock=minGQ=21(inclusive),maxGQ=22(exclusive) | |
| 27 ##GVCFBlock=minGQ=22(inclusive),maxGQ=23(exclusive) | |
| 28 ##GVCFBlock=minGQ=23(inclusive),maxGQ=24(exclusive) | |
| 29 ##GVCFBlock=minGQ=24(inclusive),maxGQ=25(exclusive) | |
| 30 ##GVCFBlock=minGQ=25(inclusive),maxGQ=26(exclusive) | |
| 31 ##GVCFBlock=minGQ=26(inclusive),maxGQ=27(exclusive) | |
| 32 ##GVCFBlock=minGQ=27(inclusive),maxGQ=28(exclusive) | |
| 33 ##GVCFBlock=minGQ=28(inclusive),maxGQ=29(exclusive) | |
| 34 ##GVCFBlock=minGQ=29(inclusive),maxGQ=30(exclusive) | |
| 35 ##GVCFBlock=minGQ=3(inclusive),maxGQ=4(exclusive) | |
| 36 ##GVCFBlock=minGQ=30(inclusive),maxGQ=31(exclusive) | |
| 37 ##GVCFBlock=minGQ=31(inclusive),maxGQ=32(exclusive) | |
| 38 ##GVCFBlock=minGQ=32(inclusive),maxGQ=33(exclusive) | |
| 39 ##GVCFBlock=minGQ=33(inclusive),maxGQ=34(exclusive) | |
| 40 ##GVCFBlock=minGQ=34(inclusive),maxGQ=35(exclusive) | |
| 41 ##GVCFBlock=minGQ=35(inclusive),maxGQ=36(exclusive) | |
| 42 ##GVCFBlock=minGQ=36(inclusive),maxGQ=37(exclusive) | |
| 43 ##GVCFBlock=minGQ=37(inclusive),maxGQ=38(exclusive) | |
| 44 ##GVCFBlock=minGQ=38(inclusive),maxGQ=39(exclusive) | |
| 45 ##GVCFBlock=minGQ=39(inclusive),maxGQ=40(exclusive) | |
| 46 ##GVCFBlock=minGQ=4(inclusive),maxGQ=5(exclusive) | |
| 47 ##GVCFBlock=minGQ=40(inclusive),maxGQ=41(exclusive) | |
| 48 ##GVCFBlock=minGQ=41(inclusive),maxGQ=42(exclusive) | |
| 49 ##GVCFBlock=minGQ=42(inclusive),maxGQ=43(exclusive) | |
| 50 ##GVCFBlock=minGQ=43(inclusive),maxGQ=44(exclusive) | |
| 51 ##GVCFBlock=minGQ=44(inclusive),maxGQ=45(exclusive) | |
| 52 ##GVCFBlock=minGQ=45(inclusive),maxGQ=46(exclusive) | |
| 53 ##GVCFBlock=minGQ=46(inclusive),maxGQ=47(exclusive) | |
| 54 ##GVCFBlock=minGQ=47(inclusive),maxGQ=48(exclusive) | |
| 55 ##GVCFBlock=minGQ=48(inclusive),maxGQ=49(exclusive) | |
| 56 ##GVCFBlock=minGQ=49(inclusive),maxGQ=50(exclusive) | |
| 57 ##GVCFBlock=minGQ=5(inclusive),maxGQ=6(exclusive) | |
| 58 ##GVCFBlock=minGQ=50(inclusive),maxGQ=51(exclusive) | |
| 59 ##GVCFBlock=minGQ=51(inclusive),maxGQ=52(exclusive) | |
| 60 ##GVCFBlock=minGQ=52(inclusive),maxGQ=53(exclusive) | |
| 61 ##GVCFBlock=minGQ=53(inclusive),maxGQ=54(exclusive) | |
| 62 ##GVCFBlock=minGQ=54(inclusive),maxGQ=55(exclusive) | |
| 63 ##GVCFBlock=minGQ=55(inclusive),maxGQ=56(exclusive) | |
| 64 ##GVCFBlock=minGQ=56(inclusive),maxGQ=57(exclusive) | |
| 65 ##GVCFBlock=minGQ=57(inclusive),maxGQ=58(exclusive) | |
| 66 ##GVCFBlock=minGQ=58(inclusive),maxGQ=59(exclusive) | |
| 67 ##GVCFBlock=minGQ=59(inclusive),maxGQ=60(exclusive) | |
| 68 ##GVCFBlock=minGQ=6(inclusive),maxGQ=7(exclusive) | |
| 69 ##GVCFBlock=minGQ=60(inclusive),maxGQ=70(exclusive) | |
| 70 ##GVCFBlock=minGQ=7(inclusive),maxGQ=8(exclusive) | |
| 71 ##GVCFBlock=minGQ=70(inclusive),maxGQ=80(exclusive) | |
| 72 ##GVCFBlock=minGQ=8(inclusive),maxGQ=9(exclusive) | |
| 73 ##GVCFBlock=minGQ=80(inclusive),maxGQ=90(exclusive) | |
| 74 ##GVCFBlock=minGQ=9(inclusive),maxGQ=10(exclusive) | |
| 75 ##GVCFBlock=minGQ=90(inclusive),maxGQ=99(exclusive) | |
| 76 ##GVCFBlock=minGQ=99(inclusive),maxGQ=2147483647(exclusive) | |
| 77 ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | |
| 78 ##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> | |
| 79 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | |
| 80 ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> | |
| 81 ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval"> | |
| 82 ##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> | |
| 83 ##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"> | |
| 84 ##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"> | |
| 85 ##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"> | |
| 86 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> | |
| 87 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> | |
| 88 ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | |
| 89 ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | |
| 90 ##contig=<ID=Chromosome,length=10000> | |
| 91 ##reference=file:///net/datasrv3hs.sanbi.ac.za/cip0/research/scratch/zahra/TB_wrk/TB_Variant_analysis/MDR/reference_H37Rv.fasta | |
| 92 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ./R_2997_878#L6-_.R | |
| 93 Chromosome 1849 . C A,<NON_REF> 4546 . DP=129;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,129,0:129:99:4576,0,4576:0,0,56,73 | |
| 94 Chromosome 1977 . A G,<NON_REF> 1957 . DP=54;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,54,0:54:99:1987,0,1987:0,0,13,41 | |
| 95 Chromosome 4013 . T C,<NON_REF> 2397 . DP=66;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,66,0:66:99:2427,0,2427:0,0,31,35 | |
| 96 Chromosome 7362 . G C,<NON_REF> 2519 . DP=68;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,68,0:68:99:2549,0,2549:0,0,28,40 | |
| 97 Chromosome 7585 . G C,<NON_REF> 1295 . DP=36;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,36,0:36:99:1325,0,1325:0,0,26,10 | |
| 98 Chromosome 9304 . G A,<NON_REF> 1945 . DP=58;MLEAC=1,0;MLEAF=1.00,0.00;MQ=70.00;MQ0=0 GT:AD:DP:GQ:PL:SB 1:0,58,0:58:99:1975,0,1975:0,0,23,35 |