Balík: picard-tools (3.1.1+dfsg-1)

Odkazy pre picard-tools

Zdroje Debian:

Stiahnuť zdrojový balík picard-tools:

Správcovia:

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

Externé zdroje:

Domovská stránka [broadinstitute.github.io]

Podobné balíky:

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

Ostatné balíky súvisiace s balíkom picard-tools

závisí

odporúča

navrhuje

vylepšuje

dep: default-jre

Standard Java or Java compatible Runtime

alebo java6-runtime

virtuálny balík poskytovaný balíkom 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

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