GATK之VariantAnnotator

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_BaseQualityRankSumTest
        AS_FisherStrand
        AS_InbreedingCoeff
        AS_InsertSizeRankSum
        AS_MQMateRankSumTest
        AS_MappingQualityRankSumTest
        AS_QualByDepth
        AS_RMSMappingQuality
        AS_ReadPosRankSumTest
        AS_StrandOddsRatio
        AlleleBalance
        BaseCounts
        *BaseQualityRankSumTest
        *ChromosomeCounts
        ClippingRankSumTest
        ClusteredReadPosition
        *Coverage
        *ExcessHet
        *FisherStrand
        FractionInformativeReads
        GCContent
        GenotypeSummaries
        *HaplotypeScore
        HardyWeinberg
        HomopolymerRun
        *InbreedingCoeff
        LikelihoodRankSumTest
        LowMQ
        MVLikelihoodRatio
        *MappingQualityRankSumTest
        MappingQualityZero
        NBaseCount
        PossibleDeNovo
        *QualByDepth
        *RMSMappingQuality
        *ReadPosRankSumTest
        SampleList
        SnpEff
        SpanningDeletions
        *StrandOddsRatio
        TandemRepeatAnnotator
        TransmissionDisequilibriumTest
        VariantType
        
Available annotations for the VCF FORMAT field:
        AlleleBalanceBySample
        AlleleCountBySample
        BaseCountsBySample
        BaseQualitySumPerAlleleBySample
        *DepthPerAlleleBySample
        DepthPerSampleHC
        MappingQualityZeroBySample
        OxoGReadCounts
        StrandAlleleCountsBySample
        StrandBiasBySample


Available classes/groups of annotations:
        AS_RMSAnnotation
        AS_RankSumTest
        AS_StandardAnnotation
        AS_StrandBiasTest
        ActiveRegionBasedAnnotation
        BetaTestingAnnotation
        ExperimentalAnnotation
        RMSAnnotation
        RankSumTest
        ReducibleAnnotation
        RodRequiringAnnotation
        StandardAnnotation
        StandardHCAnnotation
        StandardSomaticAnnotation
        StandardUGAnnotation
        StrandBiasTest
        WorkInProgressAnnotation

注释模块

这是官方文档提供的注释模块：

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