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<!doctype html> <html> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="chrome=1"> <title>Picard Tools - By Broad Institute</title> <link rel="stylesheet" href="stylesheets/styles.css"> <link rel="stylesheet" href="stylesheets/pygment_trac.css"> <script src="javascripts/scale.fix.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">  </head> <body> <div class="wrapper"> <header> <h1><a href="index.html">Picard</a></h1> <p><a href="https://travis-ci.org/broadinstitute/picard"><img src="https://travis-ci.org/broadinstitute/picard.svg?branch=master" alt="Build Status"></a></p> <p>A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.</p> <p class="view"><a href="https://github.com/broadinstitute/picard">View the Project on GitHub <small>broadinstitute/picard</small></a></p> <ul> <li><a href="https://github.com/broadinstitute/picard/releases/latest">Latest Jar <strong>Release</strong></a></li> <li><a href="https://github.com/broadinstitute/picard/zipball/master">Source Code <strong>ZIP File</strong></a></li> <li><a href="https://github.com/broadinstitute/picard/tarball/master">Source Code <strong>TAR Ball</strong></a></li> <li><a href="https://github.com/broadinstitute/picard">View On <strong>GitHub</strong></a></li> </ul> </header> <section> <p> Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the <a href="http://samtools.github.io/hts-specs/">Hts-specs</a> repository. See especially the <a href="http://samtools.github.io/hts-specs/SAMv1.pdf">SAM specification</a> and the <a href="http://samtools.github.io/hts-specs/VCFv4.3.pdf">VCF specification</a>. </p> <p> Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on <a href="https://github.com/broadinstitute/picard">GitHub</a>. </p> <p> The Picard toolkit is open-source under the <a href="https://tldrlegal.com/license/mit-license">MIT license</a> and free for all uses.</p> <p>Enjoy!</p> </section>  <h2 id="QuickStart">Quick Start</h2> <section> <h3 class='nodent'>Download Software</h3> <p> The Picard command-line tools are provided as a single executable jar file. You can download the jar file from the <a href="https://github.com/broadinstitute/picard/releases/latest"> Latest Release</a> project page on Github. The file name will be <strong>picard.jar</strong>. </p> <h3 class='nodent'>Install</h3> <p>Open the downloaded package and place the folder containing the jar file in a convenient directory on your hard drive (or server). Unlike C-compiled programs such as Samtools, Picard cannot simply be added to your PATH, so we recommend setting up an <a href="http://www.tutorialspoint.com/unix/unix-environment.htm">environment variable</a> to act as a shortcut.</p> <p>For the tools to run properly, you must have Java 1.8 installed. To check your java version by open your terminal application and run the following command: </p> <pre>java -version</pre> <p>If the output looks something like <code>java version "1.8.x"</code>, you are good to go. If not, you may need to update your version; see the <a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">Oracle Java website</a> to download the latest JDK.</p> <h3 class='nodent'>Test Installation</h3> <p>To test that you can run Picard tools, run the following command in your terminal application, providing either the full path to the picard.jar file:</p> <pre>java -jar /path/to/picard.jar -h </pre> <p>or the environment variable that you set up as a shortcut (here we are using <code>$PICARD</code>):</p> <pre>java -jar $PICARD -h </pre> <p>You should see a complete list of all the tools in the Picard toolkit. If you don't, read on to the section on Getting Help.</p> <h3 class='nodent'>Use Picard Tools</h3> <p>The tools, which are all listed further below, are invoked as follows: <pre>java jvm-args -jar picard.jar PicardToolName OPTION1=value1 OPTION2=value2...</pre> <p>See the <a href="command-line-overview.html">Tool Documentation</a> for details on the <a href="command-line-overview.html#CommandSyntax">Picard command syntax</a> and <a href="command-line-overview.html#StandardOptions">standard options</a> as well as a complete <a href="command-line-overview.html#Tools">list of tools</a> with usage recommendations, options, and example commands.</p> </section> <h2 id="GettingHelp">Getting Help</h2> <section> <p>Picard is supported through the <a href="http://gatkforums.broadinstitute.org/gatk">GATK Forums</a>. <a href="http://gatkforums.broadinstitute.org/gatk/entry/register?Target=categories%2Fgatk-support-forum">Register now</a> and you can <a href="http://gatkforums.broadinstitute.org/gatk/post/question">ask questions and report problems</a> that you might encounter while using Picard and related tools such as GATK (for source code-related questions, post an issue on <a href="https://github.com/broadinstitute/picard/issues">Github</a> instead), with the following guidelines:</p> <h3 class='nodent'>Before Asking For Help</h3> <p>Before posting to the Forum, please do the following:</p> <ul> <li>Try the <a href="https://github.com/broadinstitute/picard/releases/latest">latest version of Picard</a>.</li> <li>See if your problem is covered discussed in the <a href="http://broadinstitute.github.io/picard/faq.html">Frequently Asked Questions</a>.</li> <li>Search the <a href="http://gatkforums.broadinstitute.org/gatk">GATK Forums</a> to see if a similar problem has previously been discussed there.</li> <li>Run Picard <a href="command-line-overview.html#ValidateSamFile">ValidateSamFile</a> with MODE=SUMMARY on your input SAM or BAM file (if applicable). Attempt to resolve or at least understand any problems reported.</li> </ul> <h3 class='nodent'>When Asking For Help</h3> <p>When asking a question about a problem, please include the following:</p> <ul> <li>Command line(s) you ran</li> <li>Program console output and metrics files. Repetitive console output may be abbreviated</li> <li>Entire stack trace if one was produced</li> <li>Version of JVM you are using (obtained by running 'java -version')</li> </ul> </section> <h2 id="Resources">Additional Resources</h2> <section> <ul> <li><a href="command-line-overview.html#Overview">Detailed tool documentation</a></li> <li><a href="picard-metric-definitions.html">Description of output of metrics programs</a></li> <li><a href="sam-differences.html">SAM differences in Picard</a></li> <li><a href="explain-flags.html">Explain SAM flags</a></li> <li><a href="explain-qualities.html">Explain Base Qualities</a></li> <li><a href="http://broadinstitute.github.io/picard/javadoc/picard/index.html">Javadoc</a></li> </ul> </section> <h2 id="ListTools">Full list of Picard tools</h2> <section> <ul> <li><a href="command-line-overview.html#AddCommentsToBam">AddCommentsToBam</a> <li><a href="command-line-overview.html#AddOrReplaceReadGroups">AddOrReplaceReadGroups</a> <li><a href="command-line-overview.html#BaitDesigner">BaitDesigner</a> <li><a href="command-line-overview.html#BamToBfq">BamToBfq</a> <li><a href="command-line-overview.html#BamIndexStats">BamIndexStats</a> <li><a href="command-line-overview.html#BedToIntervalList">BedToIntervalList</a> <li><a href="command-line-overview.html#BuildBamIndex">BuildBamIndex</a> <li><a href="command-line-overview.html#CalculateReadGroupChecksum">CalculateReadGroupChecksum</a> <li><a href="command-line-overview.html#CleanSam">CleanSam</a> <li><a href="command-line-overview.html#CollectAlignmentSummaryMetrics">CollectAlignmentSummaryMetrics</a> <li><a href="command-line-overview.html#CollectBaseDistributionByCycle">CollectBaseDistributionByCycle</a> <li><a href="command-line-overview.html#CollectGcBiasMetrics">CollectGcBiasMetrics</a> <li><a href="command-line-overview.html#CollectHiSeqXPfFailMetrics">CollectHiSeqXPfFailMetrics</a> <li><a href="command-line-overview.html#CollectHsMetrics">CollectHsMetrics</a> <li><a href="command-line-overview.html#CollectIlluminaBasecallingMetrics">CollectIlluminaBasecallingMetrics</a> <li><a href="command-line-overview.html#CollectIlluminaLaneMetrics">CollectIlluminaLaneMetrics</a> <li><a href="command-line-overview.html#CollectInsertSizeMetrics">CollectInsertSizeMetrics</a> <li><a href="command-line-overview.html#CollectJumpingLibraryMetrics">CollectJumpingLibraryMetrics</a> <li><a href="command-line-overview.html#CollectMultipleMetrics">CollectMultipleMetrics</a> <li><a href="command-line-overview.html#CollectOxoGMetrics">CollectOxoGMetrics</a> <li><a href="command-line-overview.html#CollectQualityYieldMetrics">CollectQualityYieldMetrics</a> <li><a href="command-line-overview.html#CollectRawWgsMetrics">CollectRawWgsMetrics</a> <li><a href="command-line-overview.html#CollectTargetedPcrMetrics">CollectTargetedPcrMetrics</a> <li><a href="command-line-overview.html#CollectRnaSeqMetrics">CollectRnaSeqMetrics</a> <li><a href="command-line-overview.html#CollectRrbsMetrics">CollectRrbsMetrics</a> <li><a href="command-line-overview.html#CollectSequencingArtifactMetrics">CollectSequencingArtifactMetrics</a> <li><a href="command-line-overview.html#CollectVariantCallingMetrics">CollectVariantCallingMetrics</a> <li><a href="command-line-overview.html#CollectWgsMetrics">CollectWgsMetrics</a> <li><a href="command-line-overview.html#CollectWgsMetricsWithNonZeroCoverage">CollectWgsMetricsWithNonZeroCoverage</a> <li><a href="command-line-overview.html#CompareMetrics">CompareMetrics</a> <li><a href="command-line-overview.html#CompareSAMs">CompareSAMs</a> <li><a href="command-line-overview.html#ConvertSequencingArtifactToOxoG">ConvertSequencingArtifactToOxoG</a> <li><a href="command-line-overview.html#CreateSequenceDictionary">CreateSequenceDictionary</a> <li><a href="command-line-overview.html#DownsampleSam">DownsampleSam</a> <li><a href="command-line-overview.html#ExtractIlluminaBarcodes">ExtractIlluminaBarcodes</a> <li><a href="command-line-overview.html#EstimateLibraryComplexity">EstimateLibraryComplexity</a> <li><a href="command-line-overview.html#FastqToSam">FastqToSam</a> <li><a href="command-line-overview.html#FifoBuffer">FifoBuffer</a> <li><a href="command-line-overview.html#FindMendelianViolations">FindMendelianViolations</a> <li><a href="command-line-overview.html#CrosscheckFingerprints">CrosscheckFingerprints</a> <li><a href="command-line-overview.html#ClusterCrosscheckMetrics">ClusterCrosscheckMetrics</a> <li><a href="command-line-overview.html#CheckFingerprint">CheckFingerprint</a> <li><a href="command-line-overview.html#FilterSamReads">FilterSamReads</a> <li><a href="command-line-overview.html#FilterVcf">FilterVcf</a> <li><a href="command-line-overview.html#FixMateInformation">FixMateInformation</a> <li><a href="command-line-overview.html#GatherBamFiles">GatherBamFiles</a> <li><a href="command-line-overview.html#GatherVcfs">GatherVcfs</a> <li><a href="command-line-overview.html#GenotypeConcordance">GenotypeConcordance</a> <li><a href="command-line-overview.html#IlluminaBasecallsToFastq">IlluminaBasecallsToFastq</a> <li><a href="command-line-overview.html#IlluminaBasecallsToSam">IlluminaBasecallsToSam</a> <li><a href="command-line-overview.html#CheckIlluminaDirectory">CheckIlluminaDirectory</a> <li><a href="command-line-overview.html#CheckTerminatorBlock">CheckTerminatorBlock</a> <li><a href="command-line-overview.html#IntervalListTools">IntervalListTools</a> <li><a href="command-line-overview.html#LiftOverIntervalList">LiftOverIntervalList</a> <li><a href="command-line-overview.html#LiftoverVcf">LiftoverVcf</a> <li><a href="command-line-overview.html#MakeSitesOnlyVcf">MakeSitesOnlyVcf</a> <li><a href="command-line-overview.html#MarkDuplicates">MarkDuplicates</a> <li><a href="command-line-overview.html#MarkDuplicatesWithMateCigar">MarkDuplicatesWithMateCigar</a> <li><a href="command-line-overview.html#MeanQualityByCycle">MeanQualityByCycle</a> <li><a href="command-line-overview.html#MergeBamAlignment">MergeBamAlignment</a> <li><a href="command-line-overview.html#MergeSamFiles">MergeSamFiles</a> <li><a href="command-line-overview.html#MergeVcfs">MergeVcfs</a> <li><a href="command-line-overview.html#NormalizeFasta">NormalizeFasta</a> <li><a href="command-line-overview.html#PositionBasedDownsampleSam">PositionBasedDownsampleSam</a> <li><a href="command-line-overview.html#ExtractSequences">ExtractSequences</a> <li><a href="command-line-overview.html#QualityScoreDistribution">QualityScoreDistribution</a> <li><a href="command-line-overview.html#RenameSampleInVcf">RenameSampleInVcf</a> <li><a href="command-line-overview.html#ReorderSam">ReorderSam</a> <li><a href="command-line-overview.html#ReplaceSamHeader">ReplaceSamHeader</a> <li><a href="command-line-overview.html#RevertSam">RevertSam</a> <li><a href="command-line-overview.html#RevertOriginalBaseQualitiesAndAddMateCigar">RevertOriginalBaseQualitiesAndAddMateCigar</a> <li><a href="command-line-overview.html#SamFormatConverter">SamFormatConverter</a> <li><a href="command-line-overview.html#SamToFastq">SamToFastq</a> <li><a href="command-line-overview.html#ScatterIntervalsByNs">ScatterIntervalsByNs</a> <li><a href="command-line-overview.html#SetNmMdAndUqTags">SetNmMdAndUqTags</a> <li><a href="command-line-overview.html#SortSam">SortSam</a> <li><a href="command-line-overview.html#SortVcf">SortVcf</a> <li><a href="command-line-overview.html#SplitSamByLibrary">SplitSamByLibrary</a> <li><a href="command-line-overview.html#UmiAwareMarkDuplicatesWithMateCigar">UmiAwareMarkDuplicatesWithMateCigar</a> <li><a href="command-line-overview.html#UpdateVcfSequenceDictionary">UpdateVcfSequenceDictionary</a> <li><a href="command-line-overview.html#VcfFormatConverter">VcfFormatConverter</a> <li><a href="command-line-overview.html#MarkIlluminaAdapters">MarkIlluminaAdapters</a> <li><a href="command-line-overview.html#SplitVcfs">SplitVcfs</a> <li><a href="command-line-overview.html#ValidateSamFile">ValidateSamFile</a> <li><a href="command-line-overview.html#ViewSam">ViewSam</a> <li><a href="command-line-overview.html#VcfToIntervalList">VcfToIntervalList</a> </ul> </section> </div> <footer> <p>Project maintained by <a href="https://github.com/broadinstitute">broadinstitute</a></p> <p>Hosted on GitHub Pages — Theme by <a href="https://github.com/orderedlist">orderedlist</a></p> </footer>  </body> </html>