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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?