.TH picard-tools "1" "July 2010" "picard-tools 1.27" "User Commands"
.SH NAME
picard-tools \- manipulate SAM and BAM files
.SH SYNOPSIS
\fBpicard-tools\fR \fICOMMAND\fR [\fIOPTION\fR]...
.SH 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
.SH "REPORTING BUGS"
samtools-devel@lists.sourceforge.net
.SH COPYRIGHT
Copyright 2010 The Broad Institute
.SH "SEE ALSO"
http://picard.sourceforge.net/