Package: picard-tools
Version: 3.4.0+dfsg-1
Architecture: all
Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 329
Depends: default-jre | java6-runtime, libpicard-java (= 3.4.0+dfsg-1)
Section: science
Priority: optional
Homepage: https://broadinstitute.github.io/picard/
Description: Command line tools to manipulate SAM and BAM files
 SAM (Sequence Alignment/Map) format is a generic format for storing
 large nucleotide sequence alignments. Picard Tools includes these
 utilities to manipulate SAM and BAM files:
  AddCommentsToBam                  FifoBuffer
  AddOrReplaceReadGroups            FilterSamReads
  BaitDesigner                      FilterVcf
  BamIndexStats                     FixMateInformation
                                    GatherBamFiles
  BedToIntervalList                 GatherVcfs
  BuildBamIndex                     GenotypeConcordance
  CalculateHsMetrics                IlluminaBasecallsToFastq
  CalculateReadGroupChecksum        IlluminaBasecallsToSam
  CheckIlluminaDirectory            LiftOverIntervalList
  CheckTerminatorBlock              LiftoverVcf
  CleanSam                          MakeSitesOnlyVcf
  CollectAlignmentSummaryMetrics    MarkDuplicates
  CollectBaseDistributionByCycle    MarkDuplicatesWithMateCigar
  CollectGcBiasMetrics              MarkIlluminaAdapters
  CollectHiSeqXPfFailMetrics        MeanQualityByCycle
  CollectIlluminaBasecallingMetrics MergeBamAlignment
  CollectIlluminaLaneMetrics        MergeSamFiles
  CollectInsertSizeMetrics          MergeVcfs
  CollectJumpingLibraryMetrics      NormalizeFasta
  CollectMultipleMetrics            PositionBasedDownsampleSam
  CollectOxoGMetrics                QualityScoreDistribution
  CollectQualityYieldMetrics        RenameSampleInVcf
  CollectRawWgsMetrics              ReorderSam
  CollectRnaSeqMetrics              ReplaceSamHeader
  CollectRrbsMetrics                RevertOriginalBaseQualitiesAndAddMateCigar
  CollectSequencingArtifactMetrics  RevertSam
  CollectTargetedPcrMetrics         SamFormatConverter
  CollectVariantCallingMetrics      SamToFastq
  CollectWgsMetrics                 ScatterIntervalsByNs
  CompareMetrics                    SortSam
  CompareSAMs                       SortVcf
  ConvertSequencingArtifactToOxoG   SplitSamByLibrary
  CreateSequenceDictionary          SplitVcfs
  DownsampleSam                     UpdateVcfSequenceDictionary
  EstimateLibraryComplexity         ValidateSamFile
  ExtractIlluminaBarcodes           VcfFormatConverter
  ExtractSequences                  VcfToIntervalList
  FastqToSam                        ViewSam
