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)
Check Out this Related Man Page
doctools_lang_faq(n) Documentation tools doctools_lang_faq(n)
__________________________________________________________________________________________________________________________________________________NAME
doctools_lang_faq - doctools language faq
DESCRIPTION OVERVIEW
WHAT IS THIS DOCUMENT?
This document is currently mainly a placeholder, to be filled with commonly asked questions about the doctools markup language and compan-
ions, and their answers.
Please report any questions (and, if possible, answers) we should consider for this document in the category doctools of the Tcllib SF
Trackers [http://sourceforge.net/tracker/?group_id=12883].
EXAMPLES
WHERE DO I FIND DOCTOOLS EXAMPLES?
The most examples of doctools markup currently known can be found in the Tcllib and Tklib package bundles where basically the documentation
of all packages is written in it. In Tcllib you will also find the sources for the doctools documentation themselves, which makes use of
nearly all of the available markup commands. You need one of
[1] A CVS snapshot of Tcllib. How to retrieve such a snapshot and the tools required for this are described at http://source-
forge.net/cvs/?group_id=12883
[2] A Tcllib release archive. They are available at http://sourceforge.net/project/showfiles.php?group_id=12883
BUGS, IDEAS, FEEDBACK
This document, will undoubtedly contain bugs and other problems. Please report any such in the category doctools of the Tcllib SF Trackers
[http://sourceforge.net/tracker/?group_id=12883]. Please also report any ideas for enhancements you may have for either the package and/or
the documentation.
SEE ALSO
doctools_lang_cmdref, doctools_lang_intro, doctools_lang_syntax
KEYWORDS
doctools commands, doctools language, doctools markup, doctools syntax, examples, faq, markup, semantic markup
CATEGORY
Documentation tools
COPYRIGHT
Copyright (c) 2007 Andreas Kupries <andreas_kupries@users.sourceforge.net>
doctools 1.0 doctools_lang_faq(n)
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for i in 1 2 3; do
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