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picard-tools

Command line tools to manipulate SAM and BAM files

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
 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

Homepage

http://broadinstitute.github.io/picard/


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