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Picardtools

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General Description

Picard tools version 1.119

Basic Usage

module load bio #to load all bio modules
module loaf bio/picardtools/1.119 #to load picard tools alone

Useful Options

To run please type in the tool you would like to use i.e. AddCommentsToBam.  Below are a list of available tools.

AddCommentsToBam
AddOrReplaceReadGroups
BamToBfq
BamIndexStats
BedToIntervalList
BuildBamIndex
CalculateHsMetrics
CleanSam
CollectAlignmentSummaryMetrics
CollectBaseDistributionByCycle
CollectGcBiasMetrics
CollectInsertSizeMetrics
CollectMultipleMetrics
CollectTargetedPcrMetrics
CollectRnaSeqMetrics
CollectWgsMetrics
CompareSAMs
CreateSequenceDictionary
DownsampleSam
ExtractIlluminaBarcodes
EstimateLibraryComplexity
FastqToSam
FifoBuffer
FilterSamReads
FilterVcf
FixMateInformation
GatherBamFiles
GenotypeConcordance
IlluminaBasecallsToFastq
IlluminaBasecallsToSam
CheckIlluminaDirectory
IntervalListTools
LiftoverVcf
MakeSitesOnlyVcf
MarkDuplicates
MarkDuplicatesWithMateCigar
MeanQualityByCycle
MergeBamAlignment
MergeSamFiles
MergeVcfs
NormalizeFasta
ExtractSequences
QualityScoreDistribution
ReorderSam
ReplaceSamHeader
RevertSam
RevertOriginalBaseQualitiesAndAddMateCigar
SamFormatConverter
SamToFastq
SortSam
SortVcf
UpdateVcfSequenceDictionary
VcfFormatConverter
MarkIlluminaAdapters
SplitVcfs
ValidateSamFile
ViewSam
VcfToIntervalList

Further Information

See the official website: [http:// ]