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/