debian man page for picard-tools

picard-tools(1) 						   User Commands						   picard-tools(1)

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/

picard-tools 1.27						     July 2010							   picard-tools(1)