.TH picard-tools "1" "July 2013" "picard-tools 1.95" "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
 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
.SH "REPORTING BUGS"
samtools-devel@lists.sourceforge.net
.SH COPYRIGHT
Copyright 2010 The Broad Institute
.SH "SEE ALSO"
http://picard.sourceforge.net/