Tagged with #gatkdocs
97 documentation articles | 0 announcements | 3 forum discussions



Created 2012-08-15 17:00:11 | Updated 2013-03-25 18:25:50 | Tags: official gatkdocs developer walkers intermediate
Comments (0)

The GATK discovers walker documentation by reading it out of the Javadoc, Sun's design pattern for providing documentation for packages and classes. This page will provide an extremely brief explanation of how to write Javadoc; more information on writing javadoc comments can be found in Sun's documentation.

1. Adding walker and package descriptions to the help text

The GATK's build system uses the javadoc parser to extract the javadoc for classes and packages and embed the contents of that javadoc in the help system. If you add Javadoc to your package or walker, it will automatically appear in the help. The javadoc parser will pick up on 'standard' javadoc comments, such as the following, taken from PrintReadsWalker:

/**
 * This walker prints out the input reads in SAM format.  Alternatively, the walker can write reads into a specified BAM file.
 */

You can add javadoc to your package by creating a special file, package-info.java, in the package directory. This file should consist of the javadoc for your package plus a package descriptor line. One such example follows:

/**
 * @help.display.name Miscellaneous walkers (experimental)
 */
package org.broadinstitute.sting.playground.gatk.walkers;

Additionally, the GATK provides two extra custom tags for overriding the information that ultimately makes it into the help.

  • @help.display.name Changes the name of the package as it appears in help. Note that the name of the walker cannot be changed as it is required to be passed verbatim to the -T argument.

  • @help.summary Changes the description which appears on the right-hand column of the help text. This is useful if you'd like to provide a more concise description of the walker that should appear in the help.

  • @help.description Changes the description which appears at the bottom of the help text with -T <your walker> --help is specified. This is useful if you'd like to present a more complete description of your walker.

2. Hiding experimental walkers (use sparingly, please!)

Walkers can be hidden from the documentation system by adding the @Hidden annotation to the top of each walker. @Hidden walkers can still be run from the command-line, but their documentation will not be visible to end users. Please use this functionality sparingly to avoid walkers with hidden command-line options that are required for production use.

3. Disabling building of help

Because the building of our help text is actually heavyweight and can dramatically increase compile time on some systems, we have a mechanism to disable help generation.

Compile with the following command:

ant -Ddisable.help=true

to disable generation of help.


Created 2012-08-11 05:31:52 | Updated 2012-10-18 15:35:49 | Tags: official gatkdocs developer walkers intermediate
Comments (0)

The GATKDocs are what we call "Technical Documentation" in the Guide section of this website. The HTML pages are generated automatically at build time from specific blocks of documentation in the source code.

The best place to look for example documentation for a GATK walker is GATKDocsExample walker in org.broadinstitute.sting.gatk.examples. This is available here.

Below is the reproduction of that file from August 11, 2011:

/**
 * [Short one sentence description of this walker]
 *
 * <p>
 * [Functionality of this walker]
 * </p>
 *
 * <h2>Input</h2>
 * <p>
 * [Input description]
 * </p>
 *
 * <h2>Output</h2>
 * <p>
 * [Output description]
 * </p>
 *
 * <h2>Examples</h2>
 * PRE-TAG
 *    java
 *      -jar GenomeAnalysisTK.jar
 *      -T $WalkerName
 * PRE-TAG
 *
 * @category Walker Category
 * @author Your Name
 * @since Date created
 */
public class GATKDocsExample extends RodWalker<Integer, Integer> {
    /**
     * Put detailed documentation about the argument here.  No need to duplicate the summary information
     * in doc annotation field, as that will be added before this text in the documentation page.
     *
     * Notes:
     * <ul>
     *     <li>This field can contain HTML as a normal javadoc</li>
     *     <li>Don't include information about the default value, as gatkdocs adds this automatically</li>
     *     <li>Try your best to describe in detail the behavior of the argument, as ultimately confusing
     *          docs here will just result in user posts on the forum</li>
     * </ul>
     */
    @Argument(fullName="full", shortName="short", doc="Brief summary of argument [~ 80 characters of text]", required=false)
    private boolean myWalkerArgument = false;

    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
    public Integer reduceInit() { return 0; }
    public Integer reduce(Integer value, Integer sum) { return value + sum; }
    public void onTraversalDone(Integer result) { }
}

Created 2012-07-31 15:20:35 | Updated 2012-07-31 15:20:35 | Tags: gatkdocs visualizecontexttree uncategorized
Comments (0)

A new tool has been released!

Check out the documentation at VisualizeContextTree.


Created 2012-07-24 19:15:28 | Updated 2012-07-24 19:15:28 | Tags: unmatchedargumentexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at UnmatchedArgumentException.


Created 2012-07-24 19:15:27 | Updated 2012-07-24 19:15:27 | Tags: unknownenumeratedvalueexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at UnknownEnumeratedValueException.


Created 2012-07-24 19:15:27 | Updated 2012-07-24 19:15:27 | Tags: toomanyvaluesforargumentexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at TooManyValuesForArgumentException.


Created 2012-07-24 19:15:26 | Updated 2012-07-24 19:15:26 | Tags: missingargumentexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at MissingArgumentException.


Created 2012-07-24 19:15:25 | Updated 2012-07-24 19:15:25 | Tags: invalidargumentvalueexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at InvalidArgumentValueException.


Created 2012-07-24 19:15:24 | Updated 2012-07-24 19:15:24 | Tags: invalidargumentexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at InvalidArgumentException.


Created 2012-07-24 19:15:23 | Updated 2012-07-24 19:15:23 | Tags: argumentsaremutuallyexclusiveexception gatkdocs
Comments (1)

A new tool has been released!

Check out the documentation at ArgumentsAreMutuallyExclusiveException.


Created 2012-07-23 23:57:19 | Updated 2012-07-23 23:57:19 | Tags: yamagishi gatkdocs
Comments (2)

A new tool has been released!

Check out the documentation at Yamagishi.


Created 2012-07-23 23:57:18 | Updated 2012-07-23 23:57:18 | Tags: variantstovcf gatkdocs
Comments (19)

A new tool has been released!

Check out the documentation at VariantsToVCF.


Created 2012-07-23 23:57:17 | Updated 2012-07-23 23:57:17 | Tags: variantstotable gatkdocs
Comments (2)

A new tool has been released!

Check out the documentation at VariantsToTable.


Created 2012-07-23 23:57:16 | Updated 2012-07-23 23:57:16 | Tags: variantstoped gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VariantsToPED.


Created 2012-07-23 23:57:15 | Updated 2012-07-23 23:57:15 | Tags: variantstobinaryped gatkdocs
Comments (9)

A new tool has been released!

Check out the documentation at VariantsToBinaryPed.


Created 2012-07-23 23:57:15 | Updated 2012-07-23 23:57:15 | Tags: gatkdocs variantstobeagleunphased
Comments (0)

A new tool has been released!

Check out the documentation at VariantsToBeagleUnphased.


Created 2012-07-23 23:57:14 | Updated 2012-07-23 23:57:14 | Tags: variantvalidationassessor gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VariantValidationAssessor.


Created 2012-07-23 23:57:13 | Updated 2012-07-23 23:57:13 | Tags: variantrecalibratorv3 gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VariantRecalibratorV3.


Created 2012-07-23 23:57:13 | Updated 2012-07-23 23:57:13 | Tags: variantrecalibrator gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VariantRecalibrator.


Created 2012-07-23 23:57:12 | Updated 2012-07-23 23:57:12 | Tags: gatkdocs variantfiltration
Comments (0)

A new tool has been released!

Check out the documentation at VariantFiltration.


Created 2012-07-23 23:57:11 | Updated 2012-07-23 23:57:11 | Tags: variantannotator gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VariantAnnotator.


Created 2012-07-23 23:57:11 | Updated 2012-07-23 23:57:11 | Tags: gatkdocs varianteval
Comments (0)

A new tool has been released!

Check out the documentation at VariantEval.


Created 2012-07-23 23:57:10 | Updated 2012-07-23 23:57:10 | Tags: gatkdocs validationsiteselector
Comments (0)

A new tool has been released!

Check out the documentation at ValidationSiteSelector.


Created 2012-07-23 23:57:09 | Updated 2012-07-23 23:57:09 | Tags: validationamplicons gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ValidationAmplicons.


Created 2012-07-23 23:57:08 | Updated 2012-07-23 23:57:08 | Tags: gatkdocs validatingpileup
Comments (0)

A new tool has been released!

Check out the documentation at ValidatingPileup.


Created 2012-07-23 23:57:08 | Updated 2012-07-23 23:57:08 | Tags: validatevariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ValidateVariants.


Created 2012-07-23 23:57:07 | Updated 2012-07-23 23:57:07 | Tags: validaterodforreads gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ValidateRODForReads.


Created 2012-07-23 23:57:06 | Updated 2012-07-23 23:57:06 | Tags: vcfcodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VCFCodec.


Created 2012-07-23 23:57:06 | Updated 2012-07-23 23:57:06 | Tags: gatkdocs validatebaq
Comments (0)

A new tool has been released!

Check out the documentation at ValidateBAQ.


Created 2012-07-23 23:57:05 | Updated 2012-07-23 23:57:05 | Tags: vcf3codec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at VCF3Codec.


Created 2012-07-23 23:57:04 | Updated 2012-07-23 23:57:04 | Tags: unmappedreadfilter gatkdocs
Comments (4)

A new tool has been released!

Check out the documentation at UnmappedReadFilter.


Created 2012-07-23 23:57:04 | Updated 2012-07-23 23:57:04 | Tags: userexception gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at UserException.


Created 2012-07-23 23:57:03 | Updated 2012-07-23 23:57:03 | Tags: unifiedgenotyper gatkdocs
Comments (8)

A new tool has been released!

Check out the documentation at UnifiedGenotyper.


Created 2012-07-23 23:57:02 | Updated 2012-07-23 23:57:02 | Tags: ugcalclikelihoods gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at UGCalcLikelihoods.


Created 2012-07-23 23:57:02 | Updated 2012-07-23 23:57:02 | Tags: ugcallvariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at UGCallVariants.


Created 2012-07-23 23:57:01 | Updated 2012-07-23 23:57:01 | Tags: transmissiondisequilibriumtest gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at TransmissionDisequilibriumTest.


Created 2012-07-23 23:57:00 | Updated 2012-07-23 23:57:00 | Tags: gatkdocs testreadfishing
Comments (0)

A new tool has been released!

Check out the documentation at TestReadFishing.


Created 2012-07-23 23:56:59 | Updated 2012-07-23 23:56:59 | Tags: tandemrepeatannotator gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at TandemRepeatAnnotator.


Created 2012-07-23 23:56:59 | Updated 2012-07-23 23:56:59 | Tags: targetcoverageefficiency gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at TargetCoverageEfficiency.


Created 2012-07-23 23:56:58 | Updated 2012-07-23 23:56:58 | Tags: tabletovcf gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at TableToVCF.


Created 2012-07-23 23:56:57 | Updated 2012-07-23 23:56:57 | Tags: tablecodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at TableCodec.


Created 2012-07-23 23:56:57 | Updated 2012-07-23 23:56:57 | Tags: gatkdocs splitsamfile
Comments (0)

A new tool has been released!

Check out the documentation at SplitSamFile.


Created 2012-07-23 23:56:56 | Updated 2012-07-23 23:56:56 | Tags: spanningdeletions gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SpanningDeletions.


Created 2012-07-23 23:56:55 | Updated 2012-07-23 23:56:55 | Tags: gatkdocs somaticindeldetector
Comments (0)

A new tool has been released!

Check out the documentation at SomaticIndelDetector.


Created 2012-07-23 23:56:55 | Updated 2012-07-23 23:56:55 | Tags: soapsnpcodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SoapSNPCodec.


Created 2012-07-23 23:56:54 | Updated 2012-07-23 23:56:54 | Tags: snpeff gatkdocs
Comments (2)

A new tool has been released!

Check out the documentation at SnpEff.


Created 2012-07-23 23:56:53 | Updated 2012-07-23 23:56:53 | Tags: gatkdocs snpcallratebycoverage
Comments (0)

A new tool has been released!

Check out the documentation at SnpCallRateByCoverage.


Created 2012-07-23 23:56:52 | Updated 2012-07-23 23:56:52 | Tags: singlereadgroupfilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SingleReadGroupFilter.


Created 2012-07-23 23:56:52 | Updated 2012-07-23 23:56:52 | Tags: simulatereadsforvariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SimulateReadsForVariants.


Created 2012-07-23 23:56:51 | Updated 2012-07-23 23:56:51 | Tags: selectvariantsfrommongo gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SelectVariantsFromMongo.


Created 2012-07-23 23:56:50 | Updated 2012-07-23 23:56:50 | Tags: selectvariants gatkdocs
Comments (2)

A new tool has been released!

Check out the documentation at SelectVariants.


Created 2012-07-23 23:56:48 | Updated 2012-07-23 23:56:48 | Tags: selectheaders gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SelectHeaders.


Created 2012-07-23 23:56:47 | Updated 2012-07-23 23:56:47 | Tags: gatkdocs scoreseq
Comments (0)

A new tool has been released!

Check out the documentation at ScoreSeq.


Created 2012-07-23 23:56:47 | Updated 2012-07-23 23:56:47 | Tags: samplelist gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SampleList.


Created 2012-07-23 23:56:46 | Updated 2012-07-23 23:56:46 | Tags: samplefilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SampleFilter.


Created 2012-07-23 23:56:45 | Updated 2012-07-23 23:56:45 | Tags: snpdensity gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SNPDensity.


Created 2012-07-23 23:56:45 | Updated 2012-07-23 23:56:45 | Tags: samreadcodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SAMReadCodec.


Created 2012-07-23 23:56:44 | Updated 2013-03-13 01:16:25 | Tags: gatkdocs referencefastaforbedintervals
Comments (2)

This tool is not currently available to the public, sorry.


Created 2012-07-23 23:56:44 | Updated 2012-07-23 23:56:44 | Tags: sampileupcodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at SAMPileupCodec.


Created 2012-07-23 23:56:43 | Updated 2012-07-23 23:56:43 | Tags: rodthreadingperformancetest gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at RodThreadingPerformanceTest.


Created 2012-07-23 23:56:43 | Updated 2012-07-23 23:56:43 | Tags: refseqcodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at RefSeqCodec.


Created 2012-07-23 23:56:43 | Updated 2012-07-23 23:56:43 | Tags: gatkdocs rodsystemvalidation
Comments (0)

A new tool has been released!

Check out the documentation at RodSystemValidation.


Created 2012-07-23 23:56:42 | Updated 2012-07-23 23:56:42 | Tags: reassignmappingqualityfilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ReassignMappingQualityFilter.


Created 2012-07-23 23:56:42 | Updated 2012-07-23 23:56:42 | Tags: gatkdocs reducereads
Comments (1)

A new tool has been released!

Check out the documentation at ReduceReads.


Created 2012-07-23 23:56:41 | Updated 2012-07-23 23:56:41 | Tags: realignertargetcreator gatkdocs
Comments (10)

A new tool has been released!

Check out the documentation at RealignerTargetCreator.


Created 2012-07-23 23:56:40 | Updated 2012-07-23 23:56:40 | Tags: realignedreadcounter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at RealignedReadCounter.


Created 2012-07-23 23:56:39 | Updated 2012-07-23 23:56:39 | Tags: readstrandfilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ReadStrandFilter.


Created 2012-07-23 23:56:39 | Updated 2012-07-23 23:56:39 | Tags: gatkdocs readvalidation
Comments (0)

A new tool has been released!

Check out the documentation at ReadValidation.


Created 2012-07-23 23:56:38 | Updated 2012-07-23 23:56:38 | Tags: readposranksumtest gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ReadPosRankSumTest.


Created 2012-07-23 23:56:37 | Updated 2012-07-23 23:56:37 | Tags: readlengthdistribution gatkdocs
Comments (8)

A new tool has been released!

Check out the documentation at ReadLengthDistribution.


Created 2012-07-23 23:56:37 | Updated 2012-07-23 23:56:37 | Tags: readnamefilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ReadNameFilter.


Created 2012-07-23 23:56:36 | Updated 2012-07-23 23:56:36 | Tags: readgroupproperties gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ReadGroupProperties.


Created 2012-07-23 23:56:35 | Updated 2012-07-23 23:56:35 | Tags: readgroupblacklistfilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ReadGroupBlackListFilter.


Created 2012-07-23 23:56:35 | Updated 2012-07-23 23:56:35 | Tags: gatkdocs readclippingstats
Comments (0)

A new tool has been released!

Check out the documentation at ReadClippingStats.


Created 2012-07-23 23:56:34 | Updated 2012-07-23 23:56:34 | Tags: gatkdocs readbackedphasing
Comments (0)

A new tool has been released!

Check out the documentation at ReadBackedPhasing.


Created 2012-07-23 23:56:33 | Updated 2012-07-23 23:56:33 | Tags: randomlysplitvariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at RandomlySplitVariants.


Created 2012-07-23 23:56:33 | Updated 2012-07-23 23:56:33 | Tags: rawhapmapcodec gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at RawHapMapCodec.


Created 2012-07-23 23:56:32 | Updated 2012-07-23 23:56:32 | Tags: rmsmappingquality gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at RMSMappingQuality.


Created 2012-07-23 23:56:31 | Updated 2012-07-23 23:56:31 | Tags: gatkdocs quantizequals
Comments (0)

A new tool has been released!

Check out the documentation at QuantizeQuals.


Created 2012-07-23 23:56:31 | Updated 2012-07-23 23:56:31 | Tags: qualityscoredistribution gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at QualityScoreDistribution.


Created 2012-07-23 23:56:30 | Updated 2012-07-23 23:56:30 | Tags: qualbydepth gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at QualByDepth.


Created 2012-07-23 23:56:29 | Updated 2012-07-23 23:56:29 | Tags: gatkdocs qcref
Comments (0)

A new tool has been released!

Check out the documentation at QCRef.


Created 2012-07-23 23:56:29 | Updated 2012-07-23 23:56:29 | Tags: profilerodsystem gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ProfileRodSystem.


Created 2012-07-23 23:56:28 | Updated 2012-07-23 23:56:28 | Tags: gatkdocs producebeagleinput
Comments (0)

A new tool has been released!

Check out the documentation at ProduceBeagleInput.


Created 2012-07-23 23:56:27 | Updated 2012-07-23 23:56:27 | Tags: gatkdocs printreads
Comments (0)

A new tool has been released!

Check out the documentation at PrintReads.


Created 2012-07-23 23:56:25 | Updated 2012-07-23 23:56:25 | Tags: platformfilter gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at PlatformFilter.


Created 2012-07-23 23:56:05 | Updated 2012-07-23 23:56:05 | Tags: malformedreadfilter gatkdocs
Comments (9)

A new tool has been released!

Check out the documentation at MalformedReadFilter.


Created 2012-07-23 23:56:03 | Updated 2012-07-23 23:56:03 | Tags: mvlikelihoodratio gatkdocs
Comments (1)

A new tool has been released!

Check out the documentation at MVLikelihoodRatio.


Created 2012-07-23 23:55:48 | Updated 2012-07-23 23:55:48 | Tags: gatkdocs gccontentbyinterval
Comments (1)

A new tool has been released!

Check out the documentation at GCContentByInterval.


Created 2012-07-23 23:55:46 | Updated 2012-07-23 23:55:46 | Tags: gatkdocs flagstat
Comments (2)

A new tool has been released!

Check out the documentation at FlagStat.


Created 2012-07-23 23:55:39 | Updated 2012-07-23 23:55:39 | Tags: gatkdocs fastareference
Comments (2)

A new tool has been released!

Check out the documentation at FastaReference.


Created 2012-07-23 23:55:33 | Updated 2012-07-23 23:55:33 | Tags: duplicatereadfilter gatkdocs
Comments (12)

A new tool has been released!

Check out the documentation at DuplicateReadFilter.


Created 2012-07-23 23:55:29 | Updated 2013-04-12 03:10:39 | Tags: depthofcoverage gatkdocs
Comments (2)

A new tool has been released!

Check out the documentation at DepthOfCoverage.


Created 2012-07-23 23:55:10 | Updated 2012-07-23 23:55:10 | Tags: combinevariants gatkdocs
Comments (6)

A new tool has been released!

Check out the documentation at CombineVariants.


Created 2012-07-23 23:55:10 | Updated 2012-07-23 23:55:10 | Tags: gatkdocs combineduplicates
Comments (4)

A new tool has been released!

Check out the documentation at CombineDuplicates.


Created 2012-07-23 23:55:06 | Updated 2012-07-23 23:55:06 | Tags: cgvartovcf gatkdocs
Comments (7)

A new tool has been released!

Check out the documentation at CGVarToVCF.


Created 2012-07-23 23:55:01 | Updated 2012-07-23 23:55:01 | Tags: baserecalibrator gatkdocs
Comments (6)

A new tool has been released!

Check out the documentation at BaseRecalibrator.

No posts found with the requested search criteria.

Created 2013-06-11 15:36:13 | Updated | Tags: gatkdocs
Comments (4)

There are at least two images in the Guide Book that stop Adobe and give an error message. One is on page 94 the other is one page 130 Adobe says "Try..." and then gives an URL with a 32 character random alphanumeric string. LOL I am human, cannot cut and paste it (it vanishes when I try), and cannot possible type 32 random characters with our error. Could you post good URLs to these two images. Thanks


Created 2013-06-11 15:29:21 | Updated | Tags: gatkdocs
Comments (4)

Having the "Table of Contents" in the back of the GATK Guide Book, caused me considerable time and trouble. I spent hours scanning through pages, looking for topics, for several days, before I found the Table of Contents in the back. I would be surprised if I am the only one this has happened to. Could I respectfully request that you move it to the front?


Created 2012-11-06 16:13:18 | Updated | Tags: selectvariants gatkdocs genotypeconcordance
Comments (4)

I'm looking to find all the entries that change between two calls to UG on the same data. I would like to find all the entries where the call in the variant tract are different from those in the comparison track. So in effect I want those entries that would not be result from -using -conc in SelectVariants. From the documentation is is unclear if the -disc option does this:

A site is considered discordant if there exists some sample in the variant track that has a non-reference genotype and either the site isn't present in this track, the sample isn't present in this track, or the sample is called reference in this track.

What if the comp is HOM_VAR and the variant track is HET? Or if they are both HET but disagree on the specific allele?

Thanks.