picard-tools
Command line tools to manipulate SAM and BAM files
Command lineScience
Not tested on a device yet. What that means
Commands in the package
picard-toolsPicardCommandLine
About picard-tools
From Debian's package description
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
From Debian's description of the picard-tools package, under that package's license.
Dependencies
Depends on
default-jreorjava6-runtimelibpicard-java
Related apps
- samtoolsprocessing sequence alignments in SAM, BAM and CRAM formatsCommand line
fv FITS EditorView and manipulate FITS-format files- cif-toolsSuite of tools to manipulate, validate and query mmCIF filesCommand line
- bamkittools for common BAM file manipulationsCommand line
- asdftoolCommand line tool to manipulate ASDF scientific data filesCommand line
- bamtoolstoolkit for manipulating BAM (genome alignment) filesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the picard-tools package, under that package's license.
- Description: Debian's description of the picard-tools package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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