Tagged with #gatk walkers
92 documentation articles | 0 announcements | 8 forum discussions



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 (1)

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: validatevariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at ValidateVariants.


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 23:57:07 | 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: gatkdocs validatebaq
Comments (0)

A new tool has been released!

Check out the documentation at ValidateBAQ.


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 23:57:00 | 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: 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: gatkdocs splitsamfile
Comments (0)

A new tool has been released!

Check out the documentation at SplitSamFile.


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 23:56:53 | 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: 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 23:56:45 | 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 23:56:44 | 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 23:56:43 | 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 23:56:43 | 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 23:56:42 | 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: gatkdocs readvalidation
Comments (0)

A new tool has been released!

Check out the documentation at ReadValidation.


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 23:56:36 | 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: 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 23:56:31 | 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 23:56:31 | 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 23:56:29 | 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 23:56:29 | 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 23:56:28 | 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: gatkdocs printintervalsnotinbed
Comments (0)

A new tool has been released!

Check out the documentation at PrintIntervalsNotInBed.


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

A new tool has been released!

Check out the documentation at PrintRODs.


Created 2012-07-23 23:56:22 | Updated 2012-07-23 23:56:22 | Tags: gatkdocs pileup
Comments (0)

A new tool has been released!

Check out the documentation at Pileup.


Created 2012-07-23 23:56:22 | Updated 2012-07-23 23:56:22 | Tags: phasebytransmission gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at PhaseByTransmission.


Created 2012-07-23 23:56:21 | Updated 2012-07-23 23:56:21 | Tags: percent20xcoverage gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at Percent20xCoverage.


Created 2012-07-23 23:56:20 | Updated 2012-07-23 23:56:20 | Tags: gatkdocs originalqualscorehistogram
Comments (0)

A new tool has been released!

Check out the documentation at OriginalQualScoreHistogram.


Created 2012-07-23 23:56:20 | Updated 2012-07-23 23:56:20 | Tags: gatkdocs overlapwithbedininterval
Comments (0)

A new tool has been released!

Check out the documentation at OverlapWithBedInInterval.


Created 2012-07-23 23:56:18 | Updated 2012-07-23 23:56:18 | Tags: multiplylikelihoods gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at MultiplyLikelihoods.


Created 2012-07-23 23:56:17 | Updated 2012-07-23 23:56:17 | Tags: missinggenotypeerror gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at MissingGenotypeError.


Created 2012-07-23 23:56:15 | Updated 2012-07-23 23:56:15 | Tags: gatkdocs millsgenotypedecoder
Comments (0)

A new tool has been released!

Check out the documentation at MillsGenotypeDecoder.


Created 2012-07-23 23:56:10 | Updated 2012-07-23 23:56:10 | Tags: matepairlibrarysize gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at MatePairLibrarySize.


Created 2012-07-23 23:56:02 | Updated 2012-07-23 23:56:02 | Tags: gatkdocs locusmismatch
Comments (0)

A new tool has been released!

Check out the documentation at LocusMismatch.


Created 2012-07-23 23:56:01 | Updated 2012-07-23 23:56:01 | Tags: liftovervariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at LiftoverVariants.


Created 2012-07-23 23:56:00 | Updated 2012-07-23 23:56:00 | Tags: leftalignvariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at LeftAlignVariants.


Created 2012-07-23 23:56:00 | Updated 2012-07-23 23:56:00 | Tags: leftalignindels gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at LeftAlignIndels.


Created 2012-07-23 23:55:59 | Updated 2012-07-23 23:55:59 | Tags: intronlosssequencesimulator gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at IntronLossSequenceSimulator.


Created 2012-07-23 23:55:58 | Updated 2012-07-23 23:55:58 | Tags: insertsizedistribution gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at InsertSizeDistribution.


Created 2012-07-23 23:55:57 | Updated 2012-07-23 23:55:57 | Tags: gatkdocs insertrods
Comments (0)

A new tool has been released!

Check out the documentation at InsertRODs.


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

A new tool has been released!

Check out the documentation at IndelRealigner.


Created 2012-07-23 23:55:54 | Updated 2012-07-23 23:55:54 | Tags: gatkdocs iocrusher
Comments (0)

A new tool has been released!

Check out the documentation at IOCrusher.


Created 2012-07-23 23:55:50 | Updated 2012-07-23 23:55:50 | Tags: haplotyperesolver gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at HaplotypeResolver.


Created 2012-07-23 23:55:49 | Updated 2012-07-23 23:55:49 | Tags: gatkdocs greedyglgenotyper
Comments (0)

A new tool has been released!

Check out the documentation at GreedyGLGenotyper.


Created 2012-07-23 23:55:49 | Updated 2012-07-23 23:55:49 | Tags: haplotypecaller gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at HaplotypeCaller.


Created 2012-07-23 23:55:48 | Updated 2012-07-23 23:55:48 | Tags: gatkdocs genotypeandvalidate
Comments (0)

A new tool has been released!

Check out the documentation at GenotypeAndValidate.


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 23:55:48 | Updated 2012-07-23 23:55:48 | Tags: gatkdocs genenamesinterval
Comments (0)

A new tool has been released!

Check out the documentation at GeneNamesInterval.


Created 2012-07-23 23:55:46 | Updated 2012-07-23 23:55:46 | Tags: gatkpapergenotyper gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at GATKPaperGenotyper.


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 23:55:45 | Updated 2012-07-23 23:55:45 | Tags: gatkdocs fixgenotypes
Comments (0)

A new tool has been released!

Check out the documentation at FixGenotypes.


Created 2012-07-23 23:55:44 | Updated 2012-07-23 23:55:44 | Tags: fixallelesbyconcordance gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at FixAllelesByConcordance.


Created 2012-07-23 23:55:43 | Updated 2012-07-23 23:55:43 | Tags: gatkdocs findreadswithnames
Comments (0)

A new tool has been released!

Check out the documentation at FindReadsWithNames.


Created 2012-07-23 23:55:42 | Updated 2012-07-23 23:55:42 | Tags: gatkdocs findcontaminatingreadgroups
Comments (0)

A new tool has been released!

Check out the documentation at FindContaminatingReadGroups.


Created 2012-07-23 23:55:42 | Updated 2012-07-23 23:55:42 | Tags: findcoveredintervals gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at FindCoveredIntervals.


Created 2012-07-23 23:55:41 | Updated 2012-07-23 23:55:41 | Tags: filterliftedvariants gatkdocs
Comments (0)

A new tool has been released!

Check out the documentation at FilterLiftedVariants.


Created 2012-07-23 23:55:40 | Updated 2012-07-23 23:55:40 | Tags: gatkdocs fastastats
Comments (0)

A new tool has been released!

Check out the documentation at FastaStats.


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 23:55:38 | Updated 2012-07-23 23:55:38 | Tags: gatkdocs fastaalternatereference
Comments (0)

A new tool has been released!

Check out the documentation at FastaAlternateReference.


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.

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Created 2014-06-10 20:57:36 | Updated | Tags: variantannotator best-practices analyst vcf developer performance walkers java gatk
Comments (4)

Hi,

I was wondering if there is a nice way to apply multiple processing steps to each variant (or a group of variants) as they are read so that the variant file is not read again and again. My understanding is that even if I use Queue, each script would read the vcf again. Is that correct?


Created 2014-02-23 15:23:48 | Updated | Tags: variantrecalibrator
Comments (1)

Hi there,

I've a problem running GATK2.8's VariantRecalibrator, I get Code Exception (java.lang.NullPointerException). Below is the error trace:

INFO 17:05:37,528 GenomeAnalysisEngine - Preparing for traversal INFO 17:14:27,706 VariantDataManager - MQRankSum: mean = -0.09 standard deviation = 0.99 INFO 17:14:27,742 VariantDataManager - ReadPosRankSum: mean = 0.18 standard deviation = 0.96 INFO 17:14:27,820 VariantDataManager - Annotations are now ordered by their information content: [QD, ReadPosRankSum, MQRankSum] INFO 17:14:27,823 VariantDataManager - Training with 2739 variants after standard deviation thresholding. INFO 17:14:27,829 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 17:14:28,389 VariantRecalibratorEngine - Finished iteration 0. INFO 17:14:28,534 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.20522 INFO 17:14:28,601 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.46290 INFO 17:14:28,675 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 9.95604 INFO 17:14:28,759 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 9.00456 INFO 17:14:28,861 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01190 INFO 17:14:28,951 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00796 INFO 17:14:29,041 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00546 INFO 17:14:29,131 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00360 INFO 17:14:29,221 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00218 INFO 17:14:29,239 VariantRecalibratorEngine - Convergence after 46 iterations! INFO 17:14:29,276 VariantRecalibratorEngine - Evaluating full set of 13495 variants... INFO 17:14:29,280 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000. INFO 17:14:32,024 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:359) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:139) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

And this is the command i used:

java -XX:+UseParallelGC -XX:ParallelGCThreads=8 -Xmx4g -jar ~/genomekey-data/tools/gatk2.jar -T VariantRecalibrator -R ~/genomekey-data/bwa_references/human_g1k_v37.fasta -input ~/simplex/ngs_test/snp_calling/aln.haplotyper.raw.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 ~/genomekey-data/bundle/current/dbsnp_137.b37.vcf -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 ~/genomekey-data/bundle/current/hapmap_3.3.b37.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 ~/genomekey-data/bundle/current/1000G_omni2.5.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -recalFile ~/simplex/ngs_test/snp_recal/aln.snp.recal -tranche 100 -tranche 99.9 -tranche 99.0 -tranche 90 -tranchesFile ~/simplex/ngs_test/snp_recal/aln.snp.tranches -rscriptFile ~/simplex/ngs_test/snp_recal/aln.snp.plots.R -mode SNP

Please note that i got the same error running GATK 2.6. Any help or suggestions will be appreciated.

Thanks, Shazly


Created 2014-02-06 18:09:15 | Updated | Tags: developer rodwalker
Comments (7)

Is there anyway to write a sliding window RodWalker? I've been try to look in your documentation, but I have not found a clue.


Created 2013-10-05 14:15:17 | Updated | Tags: haplotypecaller
Comments (2)

Hi guys,

I am working with three genomes from the same species. I have managed to call variants between the reference and two of the genomes but the third seems to be having an issue that I don't know. I processed them exactly in the same pipeline prior to calling the variants on them using HaplotypeCaller. However, on the third genome the algorithm produces an empty vcf file as if it encountered an exact replica of the reference genome. It doesn't seem like its encountering any type of error as the log file shows that it is walking through the genome fine and the standard error file is empty (no error messages)

My code for calling the variants is as follows:

java -Xmx6g -jar Documents/GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 4 -R equcab2.fa -I Documents/PhD_work/recal.bam -stand_call_conf 20 -stand_emit_conf 10.0 -o output.raw.snps.indels.vcf 1>> gatk_HaplotypeCaller.log 2>> gatk_HaplotypeCaller.stderr

I would really appreciate if someone can help me out with this.

Thank you! :-)


Created 2013-07-10 14:19:13 | Updated | Tags: unifiedgenotyper vcf walkers
Comments (3)

I have twice run UnifiedGenotyper and the resultant .vcf file contains only part of chromosome 20. I do not see what I am doing wrong. Neither do the other two people in the lab who have extensive experience with GATKcat


Created 2013-07-09 15:32:13 | Updated | Tags: walkers
Comments (1)

I am confused about the Command-line Argument, --downsample_to_coverage. How do I know if the walker is "locus-based" or "non-locus-based"? Your on-line guide page gives an example of each but not how to identify one type of walker from another.


Created 2013-06-20 14:08:52 | Updated | Tags:
Comments (6)

The User Guide on line at this URL
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html
has this text
Example command for generating calls at all sites
...
-o my.vcf \
...
--out / -o ( VariantContextWriter with default value stdout )
File to which variants should be written. A raw, unfiltered, highly sensitive callset in VCF format.

In my hands -o my.vcf produces an error message, complaining that there is no --out
while --out my.vcf works without error

Any suggestions?


Created 2013-03-04 14:02:23 | Updated | Tags: realignertargetcreator runtime
Comments (5)

Hello,

I try to run the realigner target creator with the data divided on chromosomes. It seems to run smooth but the runtime for chromosome 1 seems to never end. I have checked my bam files and as expected the one with chr 1 is a little bit bigger than chr 2 but nothing proportional to the differences in predicted runtime. The version i use is GATK 2.3.0 and this is how i run it:

java -Xmx12g -jar programs/GenomeAnalysisTK-2.3-0/GenomeAnalysisTK.jar -l INFO -T VariantRecalibrator -R Homo_sapiens.GRCh37.57_dna_concat.fa -recalFile allchr_varrecal_BOTH_comb_ref.intervals -rscriptFile 15_allchr_varrecal_BOTH_comb_ref.intervals.plots.R -tranchesFile allchr_varrecal_BOTH_comb_ref.intervals.tranches -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf -resource:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 dbsnp_135.b37.vcf -resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ --mode BOTH -nt 8 -input allchr_real_recal_resrt_raw_BOTH_comb_ref.vcf -L Agilent_SureSelect.V4.GRCh37.70_targets_nochr.bed.pad100.interval_list --pedigreeValidationType SILENT --pedigree my_fam.fam

predicted runtime looks like:

INFO 15:11:33,778 ProgressMeter - 1:33587200 3.36e+07 2.3 h 4.1 m 1.1% 8.8 d 8.7 d INFO 15:11:33,778 ProgressMeter - 11:73495886 1.82e+09 2.3 h 4.5 s 61.0% 3.7 h 87.4 m INFO 15:11:33,778 ProgressMeter - 10:6623707 1.68e+09 2.3 h 4.9 s 54.5% 4.2 h 114.3 m INFO 15:11:33,778 ProgressMeter - 11:572298 1.82e+09 2.3 h 4.5 s 58.7% 3.9 h 96.4 m INFO 15:11:33,779 ProgressMeter - 11:122078003 1.82e+09 2.3 h 4.5 s 62.6% 3.6 h 81.7 m INFO 15:11:53,780 ProgressMeter - 11:10589211 1.82e+09 2.3 h 4.5 s 59.0% 3.9 h 95.3 m INFO 15:11:53,780 ProgressMeter - 11:105031869 1.82e+09 2.3 h 4.5 s 62.1% 3.7 h 83.9 m INFO 15:11:53,781 ProgressMeter - 11:46994477 1.82e+09 2.3 h 4.5 s 60.2% 3.8 h 90.8 m INFO 15:12:03,779 ProgressMeter - 11:8677862 1.82e+09 2.3 h 4.5 s 58.9% 3.9 h 95.7 m INFO 15:12:03,779 ProgressMeter - 11:130690257 1.82e+09 2.3 h 4.5 s 62.9% 3.6 h 81.1 m INFO 15:12:13,779 ProgressMeter - 11:84816026 1.82e+09 2.3 h 4.5 s 61.4% 3.7 h 86.4 m INFO 15:12:13,779 ProgressMeter - 10:17039143 1.68e+09 2.3 h 4.9 s 54.8% 4.2 h 113.3 m INFO 15:12:23,780 ProgressMeter - 11:18556991 1.82e+09 2.3 h 4.5 s 59.3% 3.9 h 94.6 m INFO 15:12:23,780 ProgressMeter - 11:113365440 1.82e+09 2.3 h 4.5 s 62.3% 3.7 h 83.2 m INFO 15:12:23,782 ProgressMeter - 11:55284794 1.82e+09 2.3 h 4.5 s 60.4% 3.8 h 90.1 m INFO 15:12:33,780 ProgressMeter - 1:33783808 3.38e+07 2.3 h 4.1 m 1.1% 8.8 d 8.7 d INFO 15:12:33,780 ProgressMeter - 12:3311608 1.95e+09 2.3 h 4.2 s 63.1% 3.6 h 80.5 m INFO 15:12:43,779 ProgressMeter - 11:93292307 1.82e+09 2.3 h 4.6 s 61.7% 3.7 h 85.8 m INFO 15:12:43,780 ProgressMeter - 10:24841443 1.68e+09 2.3 h 4.9 s 55.1% 4.2 h 112.5 m INFO 15:12:43,780 ProgressMeter - 11:19408689 1.82e+09 2.3 h 4.6 s 59.3% 3.9 h 94.8 m INFO 15:12:53,965 ProgressMeter - 11:26512308 1.82e+09 2.3 h 4.6 s 59.5% 3.9 h 94.0 m INFO 15:12:53,965 ProgressMeter - 11:121738354 1.82e+09 2.3 h 4.6 s 62.6% 3.7 h 82.6 m INFO 15:12:53,965 ProgressMeter - 11:63468191 1.82e+09 2.3 h 4.6 s 60.7% 3.8 h 89.4 m INFO 15:13:03,781 ProgressMeter - 12:11960820 1.95e+09 2.3 h 4.3 s 63.4% 3.6 h 79.8 m INFO 15:13:13,780 ProgressMeter - 11:101551879 1.82e+09 2.3 h 4.6 s 61.9% 3.7 h 85.1 m INFO 15:13:13,780 ProgressMeter - 10:32238974 1.68e+09 2.3 h 4.9 s 55.3% 4.2 h 111.8 m INFO 15:13:13,780 ProgressMeter - 11:27204534 1.82e+09 2.3 h 4.6 s 59.5% 3.9 h 94.1 m INFO 15:13:23,966 ProgressMeter - 11:71529440 1.82e+09 2.3 h 4.6 s 61.0% 3.8 h 88.8 m INFO 15:13:23,968 ProgressMeter - 11:34170083 1.82e+09 2.3 h 4.6 s 59.8% 3.9 h 93.4 m INFO 15:13:23,977 ProgressMeter - 11:129889715 1.82e+09 2.3 h 4.6 s 62.9% 3.7 h 81.9 m INFO 15:13:33,781 ProgressMeter - 1:33980416 3.40e+07 2.3 h 4.1 m 1.1% 8.8 d 8.7 d

Any suggestions?

Regards,

Måns