Package: picard-tools (3.1.1+dfsg-1)

Links for picard-tools

Debian Resources:

Download Source Package picard-tools:

Maintainers:

Debian Med Packaging Team (QA Page, Mail Archive)
Charles Plessy (QA Page)
Olivier Sallou (QA Page)
Vincent Danjean (QA Page)
Andreas Tille (QA Page)
Steffen Moeller (QA Page)
Pierre Gruet (QA Page)

External Resources:

Homepage [broadinstitute.github.io]

Similar packages:

Kommandolinjeværktøjer til at manipulere SAM- og BAM-filer

SAM-formatet (Sequence Alignment/Map) er et generisk format til at lagre store sammenligninger af nukleotidsekvenser. Picard Tools indeholder disse redskaber til at manipulere SAM- og BAM-filer:

 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

Other Packages Related to picard-tools

depends

recommends

suggests

enhances

dep: default-jre

Standardjava eller Javakompatibel kørselstid

or java6-runtime

virtual package provided by default-jre, openjdk-11-jre, openjdk-17-jre, openjdk-19-jre, openjdk-20-jre, openjdk-21-jre, openjdk-22-jre, openjdk-23-jre, openjdk-8-jre
dep: libpicard-java (= 3.1.1+dfsg-1)

Java library to manipulate SAM and BAM files

Download picard-tools

Download for all available architectures
Architecture	Package Size	Installed Size	Files
all	304.0 kB	329.0 kB	[list of files]