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HaplotypeCaller GVCF mode and Annotation


I wanted to run HaplotypeCaller in mode GVCF with all the possible annotations (especially I need the FisherStrand, the StrandOddsRatio and the BaseQualityRankSumTest information). For this purpose, I looked for the available annotations through this command-line:

java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.ListAnnotations

It's written that ListAnnotations is a very simple utility tool that retrieves available annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator (https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_ListAnnotations.html)

So, I ran the HaplotypeCaller with all the arguments corresponding to these annotations and I only obtained the ones that belong to the FORMAT field. I didn't obtain any annotation belonging to the INFO field (so I didn't obtain FisherStrand, StrandOddsRatio and BaseQualityRankSumTest information).

This was my command-line:

java -jar GenomeAnalysisTK-3.3-0-g37228af/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fasta -nct 1 -I one.realigned.dm.recalibrated.bam --dbsnp dbsnp_138.hg19.vcf -o one.haplotype.vcf.gz -L allkits.bed -A AlleleBalance -A BaseCounts -A BaseQualityRankSumTest -A ChromosomeCounts -A ClippingRankSumTest -A Coverage -A FisherStrand -A GCContent -A GenotypeSummaries -A HaplotypeScore -A HardyWeinberg -A HomopolymerRun -A InbreedingCoeff -A LikelihoodRankSumTest -A LowMQ -A MVLikelihoodRatio -A MappingQualityRankSumTest -A MappingQualityZero -A NBaseCount -A PossibleDeNovo -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest -A SampleList -A SnpEff -A SpanningDeletions -A StrandOddsRatio -A TandemRepeatAnnotator -A TransmissionDisequilibriumTest -A VariantType -A AlleleBalanceBySample -A AlleleCountBySample -A DepthPerAlleleBySample -A DepthPerSampleHC -A MappingQualityZeroBySample -A StrandBiasBySample --emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000 >> ~/MScall_ANNOTATION_plus.log_file 2>&1

Could you please help me with this issue?



Best Answer


  • LauraDomenechLauraDomenech BarcelonaMember

    Thanks Sheila! I'll run the GenotypeGVCFs to obtain all these annotations and if some of them does not show up, I'll let you know!


  • LauraDomenechLauraDomenech BarcelonaMember

    Hi Sheila! I need the VariantType annotation but after the GenotypeGVCFs it's gone... Do you know what's happening and how can I fix it? I need this information to filter the variants.



  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Laura,

    I just tried running GenotypeGVCFs with -A VariantType and it shows up in the output vcf. I am using version 3.4. Did you add -A VariantType to your command?


  • LauraDomenechLauraDomenech BarcelonaMember


    Yes, I added -A VariantType. You can see it in the command line that I wrote in the first comment. I used version 3.3. Can I fix it without doing all the HC again? We have a lot of samples and it took a lot of time...



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I'm not sure why the variant type annotation didn't get carried over, but you can restore it easily by running VariantAnnotator on your vcfs with -A VariantType. Note that if you're using GATK tools for filtering you don't need to explicitly set the annotation, there are some built-in functions that provide that functionality.

  • kmmahankmmahan Member

    Can -A VariantType be added to GATK4? It's currently not available in GATK4

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