[ Source: picard-tools ]
Package: picard-tools (2.8.1+dfsg-3)
Links for picard-tools
Trisquel Resources:
Download Source Package picard-tools:
- [picard-tools_2.8.1+dfsg-3.dsc]
- [picard-tools_2.8.1+dfsg.orig.tar.xz]
- [picard-tools_2.8.1+dfsg-3.debian.tar.xz]
Maintainer:
Original Maintainers:
- Debian Med Packaging Team (Mail Archive)
- Charles Plessy
- Olivier Sallou
- Vincent Danjean
- Andreas Tille
- Steffen Moeller
External Resources:
- Homepage [broadinstitute.github.io]
Similar packages:
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 BamToBfq 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
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- dep: default-jre
- Standard Java or Java compatible Runtime
- or java6-runtime
- virtual package provided by default-jre, openjdk-11-jre, openjdk-8-jre
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- dep: libpicard-java (= 2.8.1+dfsg-3)
- Java library to manipulate SAM and BAM files
Download picard-tools
| Architecture | Package Size | Installed Size | Files |
|---|---|---|---|
| all | 302.8 kB | 336 kB | [list of files] |