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)
