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

Post date: Jan 9, 2013 8:23:34 AM

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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