怎么用手机网站做软件好,网站平台建设可行性,长春建设工程管理中心网站,教育行业网站模板VariantAnnotator 简要说明 用途#xff1a; 利用上下文信息注释识别的变异位点(variant calls)分类#xff1a; 变异位点操作工具概要#xff1a; 根据变异位点的背景信息#xff08;与功能注释相对#xff09;进行注释。目前有许多的注释模块#xff08;见注释模块一节… VariantAnnotator 简要说明 用途 利用上下文信息注释识别的变异位点(variant calls)分类 变异位点操作工具概要 根据变异位点的背景信息与功能注释相对进行注释。目前有许多的注释模块见注释模块一节可供使用。 输入文件 用于注释的VCF文件和可选的BAM文件 输出文件 注释完毕的VCF文件 使用案例 对HaplotypeCaller或UnifiedGenotyper的结果中增加每个样本的深度和dbSNP ID信息。 java -jar GenomeAnalysisTK.jar \-R reference.fasta \-T VariantAnnotator \-I input.bam \-V input.vcf \-o output.vcf \-A Coverage \--dbsnp dbsnp.vcf参数说明 -R/--reference_sequence参考基因组
-T/--analysis_type 运行的工具
-I/--input_file: 和vcf相应的BAM文件
-o :输出文件
-V/--varaint 输入的VCF文件
-A/--annotation: 要添加哪些注释项
--dbsnp 已有的snp信息注释数据库注HaplotypeCaller和MuTect2也有-A选项并且有些注释模块只能在HaplotypeCaller和MuTect2计算例如StrandAlleleCountsBySample 如下是 -A可接的内容 Standard annotations in the list below are marked with a *.
Available annotations for the VCF INFO field:AS_BaseQualityRankSumTestAS_FisherStrandAS_InbreedingCoeffAS_InsertSizeRankSumAS_MQMateRankSumTestAS_MappingQualityRankSumTestAS_QualByDepthAS_RMSMappingQualityAS_ReadPosRankSumTestAS_StrandOddsRatioAlleleBalanceBaseCounts*BaseQualityRankSumTest*ChromosomeCountsClippingRankSumTestClusteredReadPosition*Coverage*ExcessHet*FisherStrandFractionInformativeReadsGCContentGenotypeSummaries*HaplotypeScoreHardyWeinbergHomopolymerRun*InbreedingCoeffLikelihoodRankSumTestLowMQMVLikelihoodRatio*MappingQualityRankSumTestMappingQualityZeroNBaseCountPossibleDeNovo*QualByDepth*RMSMappingQuality*ReadPosRankSumTestSampleListSnpEffSpanningDeletions*StrandOddsRatioTandemRepeatAnnotatorTransmissionDisequilibriumTestVariantTypeAvailable annotations for the VCF FORMAT field:AlleleBalanceBySampleAlleleCountBySampleBaseCountsBySampleBaseQualitySumPerAlleleBySample*DepthPerAlleleBySampleDepthPerSampleHCMappingQualityZeroBySampleOxoGReadCountsStrandAlleleCountsBySampleStrandBiasBySampleAvailable classes/groups of annotations:AS_RMSAnnotationAS_RankSumTestAS_StandardAnnotationAS_StrandBiasTestActiveRegionBasedAnnotationBetaTestingAnnotationExperimentalAnnotationRMSAnnotationRankSumTestReducibleAnnotationRodRequiringAnnotationStandardAnnotationStandardHCAnnotationStandardSomaticAnnotationStandardUGAnnotationStrandBiasTestWorkInProgressAnnotation注释模块 这是官方文档提供的注释模块 NameSummaryAS_BaseQualityRankSumTestAllele-specific rank Sum Test of REF versus ALT base quality scoresAS_FisherStrandAllele-specific strand bias estimated using Fishers Exact Test *AS_InbreedingCoeffAllele-specific likelihood-based test for the inbreeding among samplesAS_InsertSizeRankSumAllele specific Rank Sum Test for insert sizes of REF versus ALT readsAS_MQMateRankSumTestAllele specific Rank Sum Test for mates mapping qualities of REF versus ALT readsAS_MappingQualityRankSumTestAllele specific Rank Sum Test for mapping qualities of REF versus ALT readsAS_QualByDepthAllele-specific call confidence normalized by depth of sample reads supporting the alleleAS_RMSMappingQualityAllele-specific Root Mean Square of the mapping quality of reads across all samples.AS_ReadPosRankSumTestAllele-specific Rank Sum Test for relative positioning of REF versus ALT allele within readsAS_StrandOddsRatioAllele-specific strand bias estimated by the Symmetric Odds Ratio testAlleleBalanceAllele balance across all samplesAlleleBalanceBySampleAllele balance per sampleAlleleCountBySampleAllele count and frequency expectation per sampleBaseCountsCount of A, C, G, T bases across all samplesBaseCountsBySampleCount of A, C, G, T bases for each sampleBaseQualityRankSumTestRank Sum Test of REF versus ALT base quality scoresBaseQualitySumPerAlleleBySampleSum of evidence in reads supporting each allele for each sampleChromosomeCountsCounts and frequency of alleles in called genotypesClippingRankSumTestRank Sum Test for hard-clipped bases on REF versus ALT readsClusteredReadPositionDetect clustering of variants near the ends of readsCoverageTotal depth of coverage per sample and over all samples.DepthPerAlleleBySampleDepth of coverage of each allele per sampleDepthPerSampleHCDepth of informative coverage for each sample.ExcessHetPhred-scaled p-value for exact test of excess heterozygosityFisherStrandStrand bias estimated using Fishers Exact TestFractionInformativeReadsThe fraction of reads deemed informative over the entire cohortGCContentGC content of the reference around the given siteGenotypeSummariesSummarize genotype statistics from all samples at the site levelHaplotypeScoreConsistency of the site with strictly two segregating haplotypesHardyWeinbergHardy-Weinberg test for transmission disequilibriumHomopolymerRunLargest contiguous homopolymer run of the variant alleleInbreedingCoeffLikelihood-based test for the inbreeding among samplesLikelihoodRankSumTestRank Sum Test of per-read likelihoods of REF versus ALT readsLowMQProportion of low quality readsMVLikelihoodRatioLikelihood of being a Mendelian ViolationMappingQualityRankSumTestRank Sum Test for mapping qualities of REF versus ALT readsMappingQualityZeroCount of all reads with MAPQ 0 across all samplesMappingQualityZeroBySampleCount of reads with mapping quality zero for each sampleNBaseCountPercentage of N basesOxoGReadCountsCount of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate allelesPossibleDeNovoExistence of a de novo mutation in at least one of the given familiesQualByDepthVariant call confidence normalized by depth of sample reads supporting a variantRMSMappingQualityRoot Mean Square of the mapping quality of reads across all samples.ReadPosRankSumTestRank Sum Test for relative positioning of REF versus ALT alleles within readsSampleListList samples that are non-reference at a given siteSnpEffTop effect from SnpEff functional predictionsSpanningDeletionsFraction of reads containing spanning deletionsStrandAlleleCountsBySampleNumber of forward and reverse reads that support each alleleStrandBiasBySampleNumber of forward and reverse reads that support REF and ALT allelesStrandOddsRatioStrand bias estimated by the Symmetric Odds Ratio testTandemRepeatAnnotatorTandem repeat unit composition and counts per alleleTransmissionDisequilibriumTestWittkowski transmission disequilibrium testVariantTypeGeneral category of variant
