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/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 31 lines | 31 code | 0 blank | 0 comment | 0 complexity | 66b44d06d55adc4d68c116844b6598bb MD5 | raw file
 1##fileformat=VCFv4.1
 2##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
 3##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
 4##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
 5##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 6##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
 7##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
 8##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
 9##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
10##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
11##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
12##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
13##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
14##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
15##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
16##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
17##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
18##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
19##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">
20##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
21##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
22##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
23##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
24##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
25##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=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_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.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 debug_file=null annotation=[]"
26##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] 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 annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
27##contig=<ID=phiX174,length=5386>
28##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta
29##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta
30#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
31phiX174	1443	.	AC	.	0	.	DB;DP=10;MQ=37.74;MQ0=0	GT	./.