NAME¶

picard-tools - manipulate SAM and BAM files

SYNOPSIS¶

picard-tools COMMAND [OPTION]...

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:
AddOrReplaceReadGroups
BamToBfq
BamIndexStats
BuildBamIndex
CalculateHsMetrics
CleanSam
CollectAlignmentSummaryMetrics
CollectGcBiasMetrics
CollectInsertSizeMetrics
CollectMultipleMetrics
CollectTargetedPcrMetrics
CollectRnaSeqMetrics
CompareSAMs
CreateSequenceDictionary
DownsampleSam
ExtractIlluminaBarcodes
EstimateLibraryComplexity
FastqToSam
FilterSamReads
FixMateInformation
IlluminaBasecallsToFastq
IlluminaBasecallsToSam
CheckIlluminaDirectory
IntervalListTools
MarkDuplicates
MeanQualityByCycle
MergeBamAlignment
MergeSamFiles
MergeVcfs
NormalizeFasta
ExtractSequences
QualityScoreDistribution
ReorderSam
ReplaceSamHeader
RevertSam
SamFormatConverter
SamToFastq
SortSam
VcfFormatConverter
SplitVcfs
ValidateSamFile
ViewSam

REPORTING BUGS¶

samtools-devel@lists.sourceforge.net

COPYRIGHT¶

Copyright 2010 The Broad Institute

SEE ALSO¶

http://picard.sourceforge.net/