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 |
