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GATK - Fun - Confusion - Fear - Frustration - Things to Remember

posted Jan 9, 2013, 12:23 AM by Jonathan Keats
There are many great things about the GATK software, primarily their excellent level of support, but somethings are a bit irritating like "we change it all the time so check the --list function" which requires you to prep up a complete GATK command which can be difficult when you have no idea what you are doing.

So here are the lists I'm always wanting to have on my wall (The Genome Analysis Toolkit (GATK) v2.3-4-g57ea19f)

Variant Annotator List of Annotations
Standard annotations in the list below are marked with a '*'.

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


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


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

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