1. dagr
   1. dagr.tasks
      1. (object)
         DagrDef
      2. (object)
         DataTypes
      3. (trait)JarTask
      1. dagr.tasks.bwa
         1. (object)
            Bwa
         2. (class)BwaAln
         3. (class)BwaBacktrack
         4. (object)(class)BwaK8AltProcessor
         5. (class)BwaMem
         6. (class)BwaSampe
      2. dagr.tasks.gatk
         1. (object)(class)GatkTask
         2. (class)GenotypeSingleGvcf
         3. (class)HaplotypeCaller
         4. (class)IndelRealigner
         5. (class)IndelRealignment
         6. (class)Mutect1
         7. (class)Mutect2
         8. (class)RealignerTargetCreator
         9. (class)SplitNCigarReads
      3. dagr.tasks.jeanluc
         1. (class)FilterBam
         2. (class)GenerateRegionsFromFasta
         3. (object)(class)JeanLucTask
      4. dagr.tasks.misc
         1. (class)CalculateDownsamplingProportion
         2. (class)DeleteFiles
         3. (class)DeleteVcfs
         4. (class)GetNumPfReads
         5. (class)GetSampleNamesFromVcf
         6. (class)IndexVcfGz
         7. (class)MoveFile
         8. (object)
            Tabix
         9. (class)VerifyBamId
      5. dagr.tasks.picard
         1. (object)(class)CollectAlignmentSummaryMetrics
         2. (object)(class)CollectGcBiasMetrics
         3. (object)(class)CollectHsMetrics
         4. (object)(class)CollectInsertSizeMetrics
         5. (class)CollectMultipleMetrics
         6. (object)(class)CollectTargetedPcrMetrics
         7. (class)CollectVariantCallingMetrics
         8. (object)(class)CollectWgsMetrics
         9. (class)CopyBaiToBamBai
         10. (class)DeleteBam
         11. (class)DownsampleSam
         12. (object)
             DownsamplingStrategy
         13. (object)(class)EstimateLibraryComplexity
         14. (class)FastqToSam
         15. (object)
             FastqToUnmappedSam
         16. (class)FifoBuffer
         17. (class)FilterVcf
         18. (class)GenotypeConcordance
         19. (class)IntervalListToBed
         20. (class)IntervalListTools
         21. (object)(class)MarkDuplicates
         22. (object)(class)MarkIlluminaAdapters
         23. (class)MergeBamAlignment
         24. (class)MergeSamFiles
         25. (class)MergeVcfs
         26. (class)PicardMetricsTask
         27. (object)
             PicardOutput
         28. (object)(class)PicardTask
         29. (object)(class)SamToFastq
         30. (class)SortSam
         31. (object)(class)ValidateSamFile
      6. dagr.tasks.samtools
         1. (class)SamtoolsPileup
         2. (class)SamtoolsTask
      7. dagr.tasks.vc
         1. (object)(class)FilterFreeBayesCalls
         2. (object)(class)FreeBayes
         3. (class)FreeBayesGermline
         4. (class)FreeBayesSomatic
         5. (object)(class)Strelka
         6. (object)
            Varscan2
         7. (class)Varscan2Somatic