##FILTER=<ID=PASS,Description="All filters passed"> |
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##FILTER=<ID=LowQual,Description="Low quality"> |
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##FILTER=<ID=my_snp_filter,Description="QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"> |
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##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> |
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> |
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##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> |
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> |
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##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.7-0-gcfedb67,Date="Tue Jul 23 11:51:30 EDT 2019",Epoch=1563897090053,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[Reorder_dedup_NGTS1801253601.sam.bam.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=../../ucsc.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 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=20 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 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/external/rprshnas01/wgs_data/ALS-WES/Analysis/Reorder_dedup_NGTS1801253601.sam.bam.bam.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] 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 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 sample_name=null 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 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 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 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"> |
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##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.7-0-gcfedb67,Date="Thu Jul 25 13:08:54 EDT 2019",Epoch=1564074534110,CommandLineOptions="analysis_type=SelectVariants input_file=[] 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=../../ucsc.hg19.fasta 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=1 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 variant=(RodBinding name=variant source=Reorder_dedup_NGTS1801253601.sam.bam.bam.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/external/rprshnas01/wgs_data/ALS-WES/Analysis/rawsnps_Reorder_dedup_NGTS1801253601.sam.bam.bam.vcf.vcf sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=false preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> |
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##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.7-0-gcfedb67,Date="Thu Jul 25 14:08:22 EDT 2019",Epoch=1564078102578,CommandLineOptions="analysis_type=VariantFiltration input_file=[] 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=../../ucsc.hg19.fasta 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=1 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 variant=(RodBinding name=variant source=rawsnps_Reorder_dedup_NGTS1801253601.sam.bam.bam.vcf.vcf) mask=(RodBinding name= source=UNBOUND) out=/external/rprshnas01/wgs_data/ALS-WES/Analysis/filtered_snps_NGTS1801253601.vcf filterExpression=[QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0] filterName=[my_snp_filter] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> |
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> |
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##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> |
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
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##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> |
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##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> |
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> |
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##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> |
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##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> |
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##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> |
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##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> |
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##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"> |
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##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"> |
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##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"> |
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> |
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##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> |
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##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> |
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##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> |
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##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> |
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##contig=<ID=chrM,length=16571,assembly=hg19> |
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##contig=<ID=chr1,length=249250621,assembly=hg19> |
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##contig=<ID=chr2,length=243199373,assembly=hg19> |
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##contig=<ID=chr3,length=198022430,assembly=hg19> |
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##contig=<ID=chr4,length=191154276,assembly=hg19> |
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##contig=<ID=chr5,length=180915260,assembly=hg19> |
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##contig=<ID=chr6,length=171115067,assembly=hg19> |
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##contig=<ID=chr7,length=159138663,assembly=hg19> |
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##contig=<ID=chr8,length=146364022,assembly=hg19> |
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##contig=<ID=chr9,length=141213431,assembly=hg19> |
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##contig=<ID=chr10,length=135534747,assembly=hg19> |
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##contig=<ID=chr11,length=135006516,assembly=hg19> |
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##contig=<ID=chr12,length=133851895,assembly=hg19> |
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##contig=<ID=chr13,length=115169878,assembly=hg19> |
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##contig=<ID=chr14,length=107349540,assembly=hg19> |
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##contig=<ID=chr15,length=102531392,assembly=hg19> |
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##contig=<ID=chr16,length=90354753,assembly=hg19> |
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##contig=<ID=chr17,length=81195210,assembly=hg19> |
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##contig=<ID=chr18,length=78077248,assembly=hg19> |
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##contig=<ID=chr19,length=59128983,assembly=hg19> |
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##contig=<ID=chr20,length=63025520,assembly=hg19> |
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##contig=<ID=chr21,length=48129895,assembly=hg19> |
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##contig=<ID=chr22,length=51304566,assembly=hg19> |
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##contig=<ID=chrX,length=155270560,assembly=hg19> |
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##contig=<ID=chrY,length=59373566,assembly=hg19> |
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##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19> |
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##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19> |
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##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19> |
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##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19> |
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##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19> |
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##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19> |
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##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19> |
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##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19> |
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##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19> |
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##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19> |
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##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19> |
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##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19> |
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##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19> |
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##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19> |
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##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19> |
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##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19> |
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##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19> |
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##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19> |
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##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19> |
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##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19> |
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##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19> |
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##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19> |
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##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19> |
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##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19> |
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##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19> |
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##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19> |
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##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19> |
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##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19> |
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##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19> |
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##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19> |
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##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19> |
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##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19> |
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##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19> |
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##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19> |
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##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19> |
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##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19> |
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##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19> |
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##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19> |
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##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19> |
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##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19> |
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##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19> |
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##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19> |
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##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19> |
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##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19> |
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##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19> |
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##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19> |
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##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19> |
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##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19> |
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##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19> |
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##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19> |
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##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19> |
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##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19> |
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##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19> |
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##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19> |
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##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19> |
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##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19> |
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##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19> |
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##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19> |
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##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19> |
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##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19> |
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##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19> |
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##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19> |
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##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19> |
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##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19> |
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##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19> |
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##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19> |
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##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19> |
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##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19> |
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##reference=file:///external/rprshnas01/wgs_data/ALS-WES/Analysis/../../ucsc.hg19.fasta |
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##source=SelectVariants |
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##INFO=<ID=SpliceAI,Number=.,Type=String,Description="SpliceAI variant annotation. These include delta scores (DS) and delta positions (DP) for acceptor gain (AG), acceptor loss (AL), donor gain (DG), and donor loss (DL). Format: ALLELE|SYMBOL|DS_AG|DS_AL|DS_DG|DS_DL|DP_AG|DP_AL|DP_DG|DP_DL"> |
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#CHROM |
POS |
ID |
REF |
ALT |
QUAL |
FILTER |
INFO |
FORMAT |
chrM |
150 |
. |
T |
C |
1685.78 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=1.606;ClippingRankSum=0;DP=53;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=33.72;ReadPosRankSum=-1.21;SOR=0.693;SpliceAI=C|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
152 |
. |
T |
C |
395.77 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=-0.703;ClippingRankSum=0;DP=53;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=7.92;ReadPosRankSum=0.42;SOR=0.743;SpliceAI=C|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
184 |
. |
G |
A |
371.77 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=-0.521;ClippingRankSum=0;DP=49;ExcessHet=3.0103;FS=1.257;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=8.08;ReadPosRankSum=-0.813;SOR=0.495;SpliceAI=A|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
195 |
. |
C |
T |
1827.77 |
PASS |
AC=2;AF=1;AN=2;DP=50;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=34.04;SOR=0.874;SpliceAI=T|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
199 |
. |
T |
C |
552.77 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=0.582;ClippingRankSum=0;DP=49;ExcessHet=3.0103;FS=2.66;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=12.28;ReadPosRankSum=0.281;SOR=0.977;SpliceAI=C|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
200 |
. |
A |
G |
357.77 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=0.837;ClippingRankSum=0;DP=47;ExcessHet=3.0103;FS=4.97;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=8.32;ReadPosRankSum=0.291;SOR=1;SpliceAI=G|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
204 |
. |
T |
C |
271.77 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=0.832;ClippingRankSum=0;DP=46;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=6.47;ReadPosRankSum=0.177;SOR=0.936;SpliceAI=C|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |
chrM |
235 |
. |
A |
G |
243.77 |
PASS |
AC=1;AF=0.5;AN=2;BaseQRankSum=2.066;ClippingRankSum=0;DP=41;ExcessHet=3.0103;FS=1.448;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=6.59;ReadPosRankSum=-0.394;SOR=0.404;SpliceAI=G|.|.|.|.|.|.|.|.|. |
GT:AD:DP:GQ:PL |