VariantAnnotator

簡要說明

用途： 利用上下文信息注釋識別的變異位點(variant calls)
分類： 變異位點操作工具
概要： 根據變異位點的背景信息（與功能注釋相對）進行注釋。目前有許多的注釋模塊（見注釋模塊一節）可供使用。

輸入文件

用于注釋的VCF文件和可選的BAM文件

輸出文件

注釋完畢的VCF文件

使用案例

對HaplotypeCaller或UnifiedGenotyper的結果中增加每個樣本的深度和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

參數說明：

-R/--reference_sequence：參考基因組
-T/--analysis_type ： 運行的工具
-I/--input_file: 和vcf相應的BAM文件
-o :輸出文件
-V/--varaint： 輸入的VCF文件
-A/--annotation: 要添加哪些注釋項
--dbsnp： 已有的snp信息注釋數據庫

注HaplotypeCaller和MuTect2也有-A選項，并且有些注釋模塊只能在HaplotypeCaller和MuTect2計算，例如StrandAlleleCountsBySample
如下是 -A可接的內容：

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

注釋模塊

這是官方文檔提供的注釋模塊：

Name	Summary
AS_BaseQualityRankSumTest	Allele-specific rank Sum Test of REF versus ALT base quality scores
AS_FisherStrand	Allele-specific strand bias estimated using Fisher's Exact Test *
AS_InbreedingCoeff	Allele-specific likelihood-based test for the inbreeding among samples
AS_InsertSizeRankSum	Allele specific Rank Sum Test for insert sizes of REF versus ALT reads
AS_MQMateRankSumTest	Allele specific Rank Sum Test for mate's mapping qualities of REF versus ALT reads
AS_MappingQualityRankSumTest	Allele specific Rank Sum Test for mapping qualities of REF versus ALT reads
AS_QualByDepth	Allele-specific call confidence normalized by depth of sample reads supporting the allele
AS_RMSMappingQuality	Allele-specific Root Mean Square of the mapping quality of reads across all samples.
AS_ReadPosRankSumTest	Allele-specific Rank Sum Test for relative positioning of REF versus ALT allele within reads
AS_StrandOddsRatio	Allele-specific strand bias estimated by the Symmetric Odds Ratio test
AlleleBalance	Allele balance across all samples
AlleleBalanceBySample	Allele balance per sample
AlleleCountBySample	Allele count and frequency expectation per sample
BaseCounts	Count of A, C, G, T bases across all samples
BaseCountsBySample	Count of A, C, G, T bases for each sample
BaseQualityRankSumTest	Rank Sum Test of REF versus ALT base quality scores
BaseQualitySumPerAlleleBySample	Sum of evidence in reads supporting each allele for each sample
ChromosomeCounts	Counts and frequency of alleles in called genotypes
ClippingRankSumTest	Rank Sum Test for hard-clipped bases on REF versus ALT reads
ClusteredReadPosition	Detect clustering of variants near the ends of reads
Coverage	Total depth of coverage per sample and over all samples.
DepthPerAlleleBySample	Depth of coverage of each allele per sample
DepthPerSampleHC	Depth of informative coverage for each sample.
ExcessHet	Phred-scaled p-value for exact test of excess heterozygosity
FisherStrand	Strand bias estimated using Fisher's Exact Test
FractionInformativeReads	The fraction of reads deemed informative over the entire cohort
GCContent	GC content of the reference around the given site
GenotypeSummaries	Summarize genotype statistics from all samples at the site level
HaplotypeScore	Consistency of the site with strictly two segregating haplotypes
HardyWeinberg	Hardy-Weinberg test for transmission disequilibrium
HomopolymerRun	Largest contiguous homopolymer run of the variant allele
InbreedingCoeff	Likelihood-based test for the inbreeding among samples
LikelihoodRankSumTest	Rank Sum Test of per-read likelihoods of REF versus ALT reads
LowMQ	Proportion of low quality reads
MVLikelihoodRatio	Likelihood of being a Mendelian Violation
MappingQualityRankSumTest	Rank Sum Test for mapping qualities of REF versus ALT reads
MappingQualityZero	Count of all reads with MAPQ = 0 across all samples
MappingQualityZeroBySample	Count of reads with mapping quality zero for each sample
NBaseCount	Percentage of N bases
OxoGReadCounts	Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles
PossibleDeNovo	Existence of a de novo mutation in at least one of the given families
QualByDepth	Variant call confidence normalized by depth of sample reads supporting a variant
RMSMappingQuality	Root Mean Square of the mapping quality of reads across all samples.
ReadPosRankSumTest	Rank Sum Test for relative positioning of REF versus ALT alleles within reads
SampleList	List samples that are non-reference at a given site
SnpEff	Top effect from SnpEff functional predictions
SpanningDeletions	Fraction of reads containing spanning deletions
StrandAlleleCountsBySample	Number of forward and reverse reads that support each allele
StrandBiasBySample	Number of forward and reverse reads that support REF and ALT alleles
StrandOddsRatio	Strand bias estimated by the Symmetric Odds Ratio test
TandemRepeatAnnotator	Tandem repeat unit composition and counts per allele
TransmissionDisequilibriumTest	Wittkowski transmission disequilibrium test
VariantType	General category of variant