How To Force Output Strandbias In Gatk Unifiedgenotyper ?

Question

[kimfeng.yeung]

How to force output StrandBias in GATK UnifiedGenotyper ?

it seems that the SB (StrandBias) is a default output when the locus is a SNV, but I found that it was not output at every locus. I want SB to be output in every locus, how to type the command ?

Answer 1

[Mahdi Sarmady]

Add -A FisherStrand to your UnifiedGenotyper GATK command. It adds FisherStrand bias metric (FS) to output variants. SB is being replaced by FS. I use the following annotations as well when I run UnifiedGenotyper:

-A BaseCounts
-A AlleleBalance
-A IndelType
-A GCContent
-A NBaseCount
-A LowMQ

[Paul]

Hi everybody,

Is it possible to find list of option to use for parameter -A? I did not find it on the web.

Many Thanks,

Paul.

[Raony Guimarães]

--annotation / -A

One or more specific annotations to apply to variant calls Which annotations to add to the output VCF file. See the VariantAnnotator > -list argument to view available annotations.

Actually the full command is:

java -cp /lgc/programs/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.ListAnnotations

which gives something like this:

Available annotations for the VCF INFO field:
        AlleleBalance
        BaseCounts
        *BaseQualityRankSumTest
        *ChromosomeCounts
        ClippingRankSumTest
        *Coverage
        *FisherStrand
        GCContent
        *HaplotypeScore
        HardyWeinberg
        HomopolymerRun
        *InbreedingCoeff
        LikelihoodRankSumTest
        LowMQ
        MVLikelihoodRatio
        *MappingQualityRankSumTest
        *MappingQualityZero
        NBaseCount
        *QualByDepth
        *RMSMappingQuality
        *ReadPosRankSumTest
        SampleList
        SnpEff
        *SpanningDeletions
        StrandOddsRatio

        *TandemRepeatAnnotator
        TransmissionDisequilibriumTest
        VariantType

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

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