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
BamIndexStats
BamToBfq
BuildBamIndex
CalculateHsMetrics
CleanSam
CollectAlignmentSummaryMetrics
CollectGcBiasMetrics
CollectInsertSizeMetrics
CollectMultipleMetrics
CollectRnaSeqMetrics
CompareSAMs
CreateSequenceDictionary
ExtractIlluminaBarcodes
EstimateLibraryComplexity
ExtractSequences
FastqToSam
FixMateInformation
IlluminaBasecallsToSam
MarkDuplicates
MeanQualityByCycle
MergeBamAlignment
MergeSamFiles
NormalizeFasta
QualityScoreDistribution
ReorderSam
ReplaceSamHeader
RevertSam
SamFormatConverter
SamToFastq
SortSam
ValidateSamFile
ViewSam

REPORTING BUGS¶

samtools-devel@lists.sourceforge.net

COPYRIGHT¶

Copyright 2010 The Broad Institute

SEE ALSO¶

http://picard.sourceforge.net/