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)ClipBam
         5. (class)ClipOverlappingReads
         6. (class)CollectDuplexSeqMetrics
         7. (case class)ErrorRateByReadPosition
         8. (class)ExtractUmisFromBam
         9. (class)FastqToBam
         10. (object)(class)FgBioTask
         11. (object)(case class)FilterConsensusReads
         12. (case class)FilterSomaticVcf
         13. (class)GroupReadsByUmi
         14. (class)RemoveSamTags
         15. (class)SortBam
         16. (class)TrimFastq
         17. (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)CheckIlluminaDirectory
         2. (class)CleanSam
         3. (object)(class)CollectAlignmentSummaryMetrics
         4. (object)(class)CollectBaseDistributionByCycle
         5. (object)(class)CollectGcBiasMetrics
         6. (object)(class)CollectHsMetrics
         7. (object)(class)CollectIlluminaBasecallingMetrics
         8. (class)CollectIlluminaLaneMetrics
         9. (object)(class)CollectInsertSizeMetrics
         10. (class)CollectMultipleMetrics
         11. (object)(class)CollectQualityYieldMetrics
         12. (class)CollectSequencingArtifactMetrics
         13. (object)(class)CollectTargetedPcrMetrics
         14. (class)CollectVariantCallingMetrics
         15. (object)(class)CollectWgsMetrics
         16. (class)CopyBaiToBamBai
         17. (class)DeleteBam
         18. (class)DownsampleSam
         19. (object)
             DownsamplingStrategy
         20. (object)(class)EstimateLibraryComplexity
         21. (object)(class)ExtractIlluminaBarcodes
         22. (class)FastqToSam
         23. (object)
             FastqToUnmappedSam
         24. (class)FifoBuffer
         25. (class)FilterVcf
         26. (class)FixMateInformation
         27. (class)GatherBamFiles
         28. (class)GatherVcfs
         29. (class)GenotypeConcordance
         30. (class)IlluminaBasecallsToSam
         31. (class)IntervalListToBed
         32. (class)IntervalListTools
         33. (object)(class)MarkDuplicates
         34. (object)(class)MarkIlluminaAdapters
         35. (class)MergeBamAlignment
         36. (class)MergeSamFiles
         37. (class)MergeVcfs
         38. (trait)PicardMetricsTask
         39. (object)
             PicardOutput
         40. (object)(class)PicardTask
         41. (object)(class)RevertSam
         42. (object)(class)SamToFastq
         43. (class)SetNmAndUqTags
         44. (class)SortSam
         45. (class)SortVcf
         46. (class)UpdateVcfSequenceDictionary
         47. (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