Picard Tools
Picard Tools - By Broad Institute
http://broadinstitute.github.io/picard/command-line-overview.html
java version "1.8.x"
java -jar /path/to/picard.jar -h
Full list of Picard tools
- AddCommentsToBam
- AddOrReplaceReadGroups
- BaitDesigner
- BamToBfq
- BamIndexStats
- BedToIntervalList
- BuildBamIndex
- CalculateReadGroupChecksum
- CleanSam
- CollectAlignmentSummaryMetrics
- CollectBaseDistributionByCycle
- CollectGcBiasMetrics
- CollectHiSeqXPfFailMetrics
- CollectHsMetrics
- CollectIlluminaBasecallingMetrics
- CollectIlluminaLaneMetrics
- CollectInsertSizeMetrics
- CollectJumpingLibraryMetrics
- CollectMultipleMetrics
- CollectOxoGMetrics
- CollectQualityYieldMetrics
- CollectRawWgsMetrics
- CollectTargetedPcrMetrics
- CollectRnaSeqMetrics
- CollectRrbsMetrics
- CollectSequencingArtifactMetrics
- CollectVariantCallingMetrics
- CollectWgsMetrics
- CollectWgsMetricsWithNonZeroCoverage
- CompareMetrics
- CompareSAMs
- ConvertSequencingArtifactToOxoG
- CreateSequenceDictionary
- DownsampleSam
- ExtractIlluminaBarcodes
- EstimateLibraryComplexity
- FastqToSam
- FifoBuffer
- FindMendelianViolations
- CrosscheckFingerprints
- ClusterCrosscheckMetrics
- CheckFingerprint
- FilterSamReads
- FilterVcf
- FixMateInformation
- GatherBamFiles
- GatherVcfs
- GenotypeConcordance
- IlluminaBasecallsToFastq
- IlluminaBasecallsToSam
- CheckIlluminaDirectory
- CheckTerminatorBlock
- IntervalListTools
- LiftOverIntervalList
- LiftoverVcf
- MakeSitesOnlyVcf
- MarkDuplicates
- MarkDuplicatesWithMateCigar
- MeanQualityByCycle
- MergeBamAlignment
- MergeSamFiles
- MergeVcfs
- NormalizeFasta
- PositionBasedDownsampleSam
- ExtractSequences
- QualityScoreDistribution
- RenameSampleInVcf
- ReorderSam
- ReplaceSamHeader
- RevertSam
- RevertOriginalBaseQualitiesAndAddMateCigar
- SamFormatConverter
- SamToFastq
- ScatterIntervalsByNs
- SetNmMdAndUqTags
- SortSam
- SortVcf
- SplitSamByLibrary
- UmiAwareMarkDuplicatesWithMateCigar
- UpdateVcfSequenceDictionary
- VcfFormatConverter
- MarkIlluminaAdapters
- SplitVcfs
- ValidateSamFile
- ViewSam
- VcfToIntervalList
