GATK

VariantAnnotator

To list the available annotations:

java -jar /usr/local/GATK/GenomeAnalysisTK.jar -T VariantAnnotator -R /data/CCRBioinfo/public/GATK/bundle/1.5/hg19/ucsc.hg19.fasta -V file.vcf --list

An example list is:

Standard annotations in the list below are marked with a '*'.

Available annotations for the VCF INFO field:
	  TransmissionDisequilibriumTest
	  *ChromosomeCounts
	  IndelType
	  HardyWeinberg
	  *SpanningDeletions
	  *TandemRepeatAnnotator
	  AlleleBalance
	  LowMQ
	  BaseCounts
	  *RMSMappingQuality
	  TechnologyComposition
	  SnpEff
	  HomopolymerRun
	  *DepthOfCoverage
	  MappingQualityZeroFraction
	  NBaseCount
	  *MappingQualityZero
	  MVLikelihoodRatio
	  *InbreedingCoeff
	  *HaplotypeScore
	  SampleList
	  *QualByDepth
	  *FisherStrand
	  GCContent
	  *MappingQualityRankSumTest
	  ClippingRankSumTest
	  *ReadPosRankSumTest
	  *BaseQualityRankSumTest


Available annotations for the VCF FORMAT field:
	  AlleleBalanceBySample
	  *DepthPerAlleleBySample
	  MappingQualityZeroBySample


Available classes/groups of annotations:
	  ActiveRegionBasedAnnotation
	  RodRequiringAnnotation
	  StandardAnnotation
	  WorkInProgressAnnotation
	  ExperimentalAnnotation
	  RankSumTest

Example

java -jar /usr/local/GATK/GenomeAnalysisTK.jar -T VariantAnnotator -R /data/CCRBioinfo/public/GATK/bundle/1.5/hg19/ucsc.hg19.fasta -I AS_DNA_Normal.recal.md.realigned.bam -I AS_DNA_Tumor.recal.md.realigned.bam -V tmp.vcf -U -o tmp.gatk.vcf -A AlleleBalanceBySample -A MappingQualityZeroBySample -A MappingQualityZero -A QualByDepth -A ReadPosRankSumTest -A BaseQualityRankSumTest -A HaplotypeScore -A RMSMappingQuality -A LowMQ -A HomopolymerRun -A BaseCounts