1. dagr
   1. dagr.tasks
      1. (object)
         DagrDef
      2. (object)
         DataTypes
      3. (object)(trait)JarTask
      4. (object)
         ScatterGather
      1. dagr.tasks.bwa
         1. (object)
            Bwa
         2. (class)BwaAln
         3. (class)BwaBacktrack
         4. (class)BwaIndex
         5. (object)(class)BwaK8AltProcessor
         6. (class)BwaMem
         7. (class)BwaSampe
         8. (class)BwaSamse
      2. dagr.tasks.fgbio
         1. (object)
            AssignmentStrategy
         2. (class)CallDuplexConsensusReads
         3. (class)CallMolecularConsensusReads
         4. (class)ClipOverlappingReads
         5. (case class)ErrorRateByReadPosition
         6. (class)ExtractUmisFromBam
         7. (object)(class)FgBioTask
         8. (object)(case class)FilterConsensusReads
         9. (case class)FilterSomaticVcf
         10. (class)GroupReadsByUmi
         11. (class)RemoveSamTags
         12. (class)TrimFastq
         13. (class)TrimPrimers
      3. dagr.tasks.gatk
         1. (object)(class)GatkTask
         2. (object)(class)GenotypeGvcfs
         3. (class)HaplotypeCaller
         4. (class)IndelRealigner
         5. (object)(class)IndelRealignment
         6. (class)Mutect1
         7. (class)Mutect2
         8. (class)RealignerTargetCreator
         9. (class)SplitIntervalsForCallingRegions
         10. (class)SplitNCigarReads
      4. dagr.tasks.jeanluc
         1. (class)FilterBam
         2. (class)GenerateRegionsFromFasta
         3. (object)(class)JeanLucTask
      5. dagr.tasks.misc
         1. (class)CalculateDownsamplingProportion
         2. (class)DeleteFiles
         3. (class)DeleteVcfs
         4. (class)GetNumPfReads
         5. (class)GetSampleNamesFromVcf
         6. (class)IndexVcfGz
         7. (class)MakeDirectory
         8. (class)MoveFile
         9. (object)
            Tabix
         10. (class)VerifyBamId
      6. dagr.tasks.picard
         1. (class)CleanSam
         2. (object)(class)CollectAlignmentSummaryMetrics
         3. (object)(class)CollectGcBiasMetrics
         4. (object)(class)CollectHsMetrics
         5. (object)(class)CollectInsertSizeMetrics
         6. (class)CollectMultipleMetrics
         7. (class)CollectSequencingArtifactMetrics
         8. (object)(class)CollectTargetedPcrMetrics
         9. (class)CollectVariantCallingMetrics
         10. (object)(class)CollectWgsMetrics
         11. (class)CopyBaiToBamBai
         12. (class)DeleteBam
         13. (class)DownsampleSam
         14. (object)
             DownsamplingStrategy
         15. (object)(class)EstimateLibraryComplexity
         16. (class)FastqToSam
         17. (object)
             FastqToUnmappedSam
         18. (class)FifoBuffer
         19. (class)FilterVcf
         20. (class)FixMateInformation
         21. (class)GatherBamFiles
         22. (class)GatherVcfs
         23. (class)GenotypeConcordance
         24. (class)IntervalListToBed
         25. (class)IntervalListTools
         26. (object)(class)MarkDuplicates
         27. (object)(class)MarkIlluminaAdapters
         28. (class)MergeBamAlignment
         29. (class)MergeSamFiles
         30. (class)MergeVcfs
         31. (trait)PicardMetricsTask
         32. (object)
             PicardOutput
         33. (object)(class)PicardTask
         34. (object)(class)RevertSam
         35. (object)(class)SamToFastq
         36. (class)SetNmAndUqTags
         37. (class)SortSam
         38. (class)SortVcf
         39. (class)UpdateVcfSequenceDictionary
         40. (object)(class)ValidateSamFile
      7. dagr.tasks.samtools
         1. (class)SamtoolsFaidx
         2. (class)SamtoolsPileup
         3. (class)SamtoolsTask
      8. dagr.tasks.vc
         1. (object)(class)FilterFreeBayesCalls
         2. (object)(class)FreeBayes
         3. (class)FreeBayesGermline
         4. (class)FreeBayesParallel
         5. (class)FreeBayesSomatic
         6. (object)(class)Strelka
         7. (object)
            VarDictJava
         8. (class)VarDictJavaEndToEnd
         9. (object)
            Varscan2
         10. (class)Varscan2Somatic