mirror of
https://github.com/chenasraf/snpr.git
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Adds test and testdata for new parsing for 23andme-exome-vcf
This commit is contained in:
Philipp Bayer
@@ -18,6 +18,44 @@ describe 'genotype parsing', sidekiq: :inline do
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expect(Snp.count).to be_zero
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end
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context '23andMe-exome-vcf' do
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let(:file) { File.open(Rails.root.join('test/data/23andmeexome_test.csv')) }
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let(:genotype) do
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create(:genotype, genotype: file, filetype: '23andme-exome-vcf')
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end
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it 'parses 23andMe exome vcf data', truncate: true do
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snp_data = Snp.all.map do |s|
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[s.name, s.position, s.chromosome, s.genotype_frequency,
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s.allele_frequency, s.ranking]
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end
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snp_data = snp_data.sort_by { |s| s[0] }
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expected = [
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['rs79585140', '14907', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs75454623', '14930', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs71252250', '15118', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs75062661', '69511', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs142727405', '663097', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs144155419', '717587', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs3131972', '752721', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs61770172', '753269', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
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['rs61770173', '753405', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0]
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]
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expect(snp_data).to match_array(expected)
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user_snps = UserSnp.all
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user_snp_genotypes = user_snps.map(&:local_genotype)
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expected_genotypes = %w(AG AG AG GG CC AA AG GG AA)
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expect(user_snp_genotypes).to eq(expected_genotypes)
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user_snps.each do |s|
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expect(s.genotype_id).to eq(genotype.id)
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expect(Snp.pluck(:name)).to include(s.snp_name)
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end
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end
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end
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context '23andMe' do
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let(:file) { File.open(Rails.root.join('test/data/23andMe_test.csv')) }
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let(:genotype) do
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151
test/data/23andmeexome_test.csv
Normal file
151
test/data/23andmeexome_test.csv
Normal file
@@ -0,0 +1,151 @@
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##fileformat=VCFv4.1
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##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/creph/gspipe/data/opt/ref_genome/gspipe/0.1/genomes/G1K.37/G1K.37.nt.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false 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=LF5792_vars_v1.cs.INDEL.vcf), (RodBinding name=variant2 source=LF5792_vars_v1.cs.SNP.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 rod_priority_list=variant2,variant printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=null assumeIdenticalSamples=true minimumN=1 mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
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##FILTER=<ID=FSFilter200,Description="FS > 200.0">
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##FILTER=<ID=FSFilter60,Description="FS > 60.0">
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##FILTER=<ID=HaplotypeScoreFilter13,Description="HaplotypeScore > 13.0">
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##FILTER=<ID=InbreedingCoeff0_8,Description="InbreedingCoeff < -0.8">
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##FILTER=<ID=MQFilter40,Description="MQ < 40.0">
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##FILTER=<ID=MQRankSumFilter12_5,Description="MQRankSum < -12.5">
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##FILTER=<ID=QDFilter2,Description="QD < 2.0">
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##FILTER=<ID=ReadPosRankSumFilter20,Description="ReadPosRankSum < -20.0">
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##FILTER=<ID=ReadPosRankSumFilter8,Description="ReadPosRankSum < -8.0">
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##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
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##FORMAT=<ID=AD,Number=.,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=Float,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=PL,Number=.,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
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##INFO=<ID=AC,Number=.,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=.,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=DB,Number=0,Type=Flag,Description="dbSNP Membership">
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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=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
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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=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
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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=IndelType,Number=1,Type=String,Description="Indel type description">
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##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
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##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
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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=SNPEFF_AMINO_ACID_CHANGE,Number=1,Type=String,Description="Old/New amino acid for the highest-impact effect resulting from the current variant (in HGVS style)">
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##INFO=<ID=SNPEFF_CODON_CHANGE,Number=1,Type=String,Description="Old/New codon for the highest-impact effect resulting from the current variant">
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##INFO=<ID=SNPEFF_EFFECT,Number=1,Type=String,Description="The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)">
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##INFO=<ID=SNPEFF_EXON_ID,Number=1,Type=String,Description="Exon ID for the highest-impact effect resulting from the current variant">
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##INFO=<ID=SNPEFF_FUNCTIONAL_CLASS,Number=1,Type=String,Description="Functional class of the highest-impact effect resulting from the current variant: [NONE, SILENT, MISSENSE, NONSENSE]">
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##INFO=<ID=SNPEFF_GENE_BIOTYPE,Number=1,Type=String,Description="Gene biotype for the highest-impact effect resulting from the current variant">
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##INFO=<ID=SNPEFF_GENE_NAME,Number=1,Type=String,Description="Gene name for the highest-impact effect resulting from the current variant">
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##INFO=<ID=SNPEFF_IMPACT,Number=1,Type=String,Description="Impact of the highest-impact effect resulting from the current variant [MODIFIER, LOW, MODERATE, HIGH]">
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##INFO=<ID=SNPEFF_TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID for the highest-impact effect resulting from the current variant">
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##OriginalSnpEffCmd="SnpEff eff GRCh37.64 -config /creph/gspipe/data/opt/app/snpEff/2.0.5/snpEff.config -onlyCoding true -o vcf -i vcf LF5792_vars.cs.vcf "
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##OriginalSnpEffVersion="2.0.5 (build 2011-12-24), by Pablo Cingolani"
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##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/creph/gspipe/data/opt/ref_genome/gspipe/0.1/genomes/G1K.37/G1K.37.nt.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false 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=LF5792_vars_snpeff.cs.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) 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 sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null outMVFile=null filter_mismatching_base_and_quals=false"
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##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[./LF5792_recalaln.cs.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/creph/gspipe/data/opt/platform/agilent/50Mb/targets_merged_250.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/creph/gspipe/data/opt/ref_genome/gspipe/0.1/genomes/G1K.37/G1K.37.nt.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=CALCULATE_AS_NECESSARY baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false 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 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=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name=dbsnp source=/creph/gspipe/data/opt/variant/dbSNP/b135/dbSNP.b135.vcf.gz) 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=[FisherStrand, DepthOfCoverage, BaseQualityRankSumTest, ChromosomeCounts, IndelType, SpanningDeletions, AlleleBalance, MappingQualityZero, HaplotypeScore, QualByDepth, HomopolymerRun, MappingQualityRankSumTest, ReadPosRankSumTest, BaseQualityRankSumTest] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
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##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/creph/gspipe/data/opt/ref_genome/gspipe/0.1/genomes/G1K.37/G1K.37.nt.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false 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=LF5792_vars.cs.vcf) snpEffFile=(RodBinding name=variant2 source=-) dbsnp=(RodBinding name= source=UNBOUND) 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=[SnpEff] excludeAnnotation=[] group=[] expression=[] useAllAnnotations=false list=false vcfContainsOnlyIndels=false MendelViolationGenotypeQualityThreshold=0.0 requireStrictAlleleMatch=false filter_mismatching_base_and_quals=false"
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##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/creph/gspipe/data/opt/ref_genome/gspipe/0.1/genomes/G1K.37/G1K.37.nt.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false 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=SNP.selected.vcf) mask=(RodBinding name= source=UNBOUND) 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 filterExpression=[QD < 2.0, MQ < 40.0, FS > 60.0, HaplotypeScore > 13.0, MQRankSum < -12.5, ReadPosRankSum < -8.0] filterName=[QDFilter2, MQFilter40, FSFilter60, HaplotypeScoreFilter13, MQRankSumFilter12_5, ReadPosRankSumFilter8] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=10 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false filter_mismatching_base_and_quals=false"
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##contig=<ID=GL000249.1,length=38502>
|
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##contig=<ID=MT,length=16569>
|
||||
##contig=<ID=X,length=155270560>
|
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##contig=<ID=Y,length=59373566>
|
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##reference=file:///creph/gspipe/data/opt/ref_genome/gspipe/0.1/genomes/G1K.37/G1K.37.nt.fasta
|
||||
##source=SelectVariants
|
||||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LF5792
|
||||
1 14653 . C T 31.99 MQFilter40;QDFilter2 AB=0.681;AC=1;AF=0.50;AN=2;BaseQRankSum=0.971;DP=69;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=9.29;MQ0=51;MQRankSum=0.265;QD=0.46;ReadPosRankSum=-0.618;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=DDX11L1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000450305 GT:AD:DP:GQ:PL 0/1:47,22:69:61.98:62,0,89
|
||||
1 14907 rs79585140 A G 1133.38 MQFilter40 AB=0.353;AC=1;AF=0.50;AN=2;BaseQRankSum=-1.1;DB;DP=116;Dels=0.0;FS=1.008;HRun=1;HaplotypeScore=1.8455;MQ=29.59;MQ0=10;MQRankSum=0.731;QD=9.77;ReadPosRankSum=0.849;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=DDX11L1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000450305 GT:AD:DP:GQ:PL 0/1:41,75:116:99:1163,0,620
|
||||
1 14930 rs75454623 A G 1362.98 MQFilter40 AB=0.319;AC=1;AF=0.50;AN=2;BaseQRankSum=-4.527;DB;DP=136;Dels=0.01;FS=1.885;HRun=0;HaplotypeScore=11.2891;MQ=30.93;MQ0=0;MQRankSum=0.104;QD=9.95;ReadPosRankSum=-1.572;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=DDX11L1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000450305 GT:AD:DP:GQ:PL 0/1:43,92:136:99:1393,0,698
|
||||
1 15118 rs71252250 A G 63.69 MQFilter40;QDFilter2 AB=0.744;AC=1;AF=0.50;AN=2;BaseQRankSum=2.418;DB;DP=44;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=1.4972;MQ=15.01;MQ0=17;MQRankSum=1.252;QD=1.45;ReadPosRankSum=-0.379;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=DDX11L1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000450305 GT:AD:DP:GQ:PL 0/1:32,11:44:93.68:94,0,135
|
||||
1 17538 . C A 121.99 MQFilter40;QDFilter2 AB=0.864;AC=1;AF=0.50;AN=2;BaseQRankSum=-1.591;DP=82;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=1.8288;MQ=28.2;MQ0=28;MQRankSum=-0.253;QD=1.49;ReadPosRankSum=0.0;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=DDX11L1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000450305 GT:AD:DP:GQ:PL 0/1:70,11:82:99:152,0,1232
|
||||
1 69270 . A G 74.12 MQFilter40;QDFilter2 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=3.28;MQ0=241;QD=0.3;SNPEFF_AMINO_ACID_CHANGE=S108;SNPEFF_CODON_CHANGE=tcA/tcG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_69037_69829;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=OR4F5;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000534990 GT:AD:DP:GQ:PL 1/1:207,35:250:11.99:107,12,0
|
||||
1 69511 rs75062661 A G 1354.06 MQFilter40 AC=2;AF=1.00;AN=2;DB;DP=95;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.9665;MQ=25.29;MQ0=10;QD=14.25;SNPEFF_AMINO_ACID_CHANGE=T141A;SNPEFF_CODON_CHANGE=Aca/Gca;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_69091_70008;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=OR4F5;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000335137 GT:AD:DP:GQ:PL 1/1:1,93:95:99:1387,141,0
|
||||
1 663097 rs142727405 G C 39.61 MQFilter40 AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=23.33;MQ0=2;QD=4.95;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_pseudogene;SNPEFF_GENE_NAME=CICP3;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000440782 GT:AD:DP:GQ:PL 1/1:3,5:8:6.02:71,6,0
|
||||
1 717587 rs144155419 G A 79.91 PASS AB=0.714;AC=1;AF=0.50;AN=2;BaseQRankSum=-0.495;DB;DP=14;Dels=0.0;FS=2.963;HRun=2;HaplotypeScore=0.0;MQ=52.61;MQ0=0;MQRankSum=0.495;QD=5.71;ReadPosRankSum=0.354;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AL669831.1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000358533 GT:AD:DP:GQ:PL 0/1:10,4:14:99:110,0,345
|
||||
1 752721 rs3131972 A G 58.29 MQFilter40 AB=0.25;AC=1;AF=0.50;AN=2;BaseQRankSum=-0.727;DB;DP=4;Dels=0.0;FS=0.0;HRun=3;HaplotypeScore=0.0;MQ=29.0;MQ0=0;MQRankSum=0.727;QD=14.57;ReadPosRankSum=0.727;SNPEFF_EFFECT=TRANSCRIPT;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=RP11-206L10.10;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000435300 GT:AD:DP:GQ:PL 0/1:1,3:4:21.40:88,0,21
|
||||
1 753269 rs61770172 C G 704.16 MQFilter40 AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=19.61;MQ0=35;QD=10.83;SNPEFF_EFFECT=TRANSCRIPT;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=FAM87B;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000326734 GT:AD:DP:GQ:PL 1/1:0,65:65:66.16:737,66,0
|
||||
1 753405 rs61770173 C A 54.43 MQFilter40;QDFilter2 AB=0.75;AC=1;AF=0.50;AN=2;BaseQRankSum=3.873;DB;DP=35;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.8667;MQ=37.88;MQ0=1;MQRankSum=-2.812;QD=1.56;ReadPosRankSum=-2.016;SNPEFF_EFFECT=TRANSCRIPT;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=FAM87B;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000326734 GT:AD:DP:GQ:PL 0/1:24,8:35:84.42:84,0,599
|
||||
1 884091 rs142735174 C CACCCTGGTCCCCCTGGTCC 98.52 PASS AB=0.536;AC=1;AF=0.50;AN=2;BaseQRankSum=0.259;DB;DP=15;FS=0.0;HRun=0;HaplotypeScore=284.6099;IndelType=I;MQ=49.09;MQ0=0;MQRankSum=1.813;QD=6.57;ReadPosRankSum=2.205;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066 GT:AD:DP:GQ:PL 0/1:2,4:15:99:138,0,769
|
||||
|
Can't render this file because it contains an unexpected character in line 2 and column 19.
|
Reference in New Issue
Block a user