21:17:28.690 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-40db79c-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
21:17:28.807 INFO OmitFromCommandLineCLP - ------------------------------------------------------------
21:17:28.811 INFO OmitFromCommandLineCLP - The Genome Analysis Toolkit (GATK) v4.6.1.0-11-g40db79c-SNAPSHOT
21:17:28.812 INFO OmitFromCommandLineCLP - For support and documentation go to https://software.broadinstitute.org/gatk/
21:17:28.812 INFO OmitFromCommandLineCLP - Executing as root@947a58c13613 on Linux v6.8.0-1020-azure amd64
21:17:28.812 INFO OmitFromCommandLineCLP - Java runtime: OpenJDK 64-Bit Server VM v17.0.12+7-Ubuntu-1ubuntu222.04
21:17:28.813 INFO OmitFromCommandLineCLP - Start Date/Time: February 10, 2025 at 9:17:28 PM GMT
21:17:28.813 INFO OmitFromCommandLineCLP - ------------------------------------------------------------
21:17:28.813 INFO OmitFromCommandLineCLP - ------------------------------------------------------------
21:17:28.814 INFO OmitFromCommandLineCLP - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:17:28.814 INFO OmitFromCommandLineCLP - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:17:28.814 INFO OmitFromCommandLineCLP - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:17:28.815 INFO OmitFromCommandLineCLP - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:17:28.815 INFO OmitFromCommandLineCLP - Deflater: IntelDeflater
21:17:28.815 INFO OmitFromCommandLineCLP - Inflater: IntelInflater
21:17:28.815 INFO OmitFromCommandLineCLP - GCS max retries/reopens: 20
21:17:28.815 INFO OmitFromCommandLineCLP - Requester pays: disabled
21:17:28.815 INFO OmitFromCommandLineCLP - Initializing engine
21:17:28.816 INFO OmitFromCommandLineCLP - Done initializing engine
21:17:28.816 INFO OmitFromCommandLineCLP - Shutting down engine
[February 10, 2025 at 9:17:28 PM GMT] org.broadinstitute.hellbender.MainTest$OmitFromCommandLineCLP done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
?[1m?[31mUSAGE: ?[32m<program name>?[1m?[31m [-h]
?[0m?[1m?[31mAvailable Programs:
?[0m?[37m--------------------------------------------------------------------------------------
?[0m?[31mBase Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters?[0m
?[32m CheckIlluminaDirectory (Picard) ?[36mAsserts the validity for specified Illumina basecalling data. ?[0m
?[32m CollectIlluminaBasecallingMetrics (Picard) ?[36mCollects Illumina Basecalling metrics for a sequencing run. ?[0m
?[32m CollectIlluminaLaneMetrics (Picard) ?[36mCollects Illumina lane metrics for the given BaseCalling analysis directory.?[0m
?[32m ExtractIlluminaBarcodes (Picard) ?[36mTool determines the barcode for each read in an Illumina lane. ?[0m
?[32m IlluminaBasecallsToFastq (Picard) ?[36mGenerate FASTQ file(s) from Illumina basecall read data. ?[0m
?[32m IlluminaBasecallsToSam (Picard) ?[36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.?[0m
?[32m MarkIlluminaAdapters (Picard) ?[36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mCopy Number Variant Discovery: Tools that analyze read coverage to detect copy number variants.?[0m
?[32m AnnotateIntervals ?[36mAnnotates intervals with GC content, mappability, and segmental-duplication content?[0m
?[32m CallCopyRatioSegments ?[36mCalls copy-ratio segments as amplified, deleted, or copy-number neutral?[0m
?[32m CombineSegmentBreakpoints ?[31m(EXPERIMENTAL Tool) ?[36mCombine the breakpoints of two segment files and annotate the resulting intervals with chosen columns from each file.?[0m
?[32m CreateReadCountPanelOfNormals ?[36mCreates a panel of normals for read-count denoising?[0m
?[32m DenoiseReadCounts ?[36mDenoises read counts to produce denoised copy ratios?[0m
?[32m DetermineGermlineContigPloidy ?[36mDetermines the baseline contig ploidy for germline samples given counts data?[0m
?[32m FilterIntervals ?[36mFilters intervals based on annotations and/or count statistics?[0m
?[32m GermlineCNVCaller ?[36mCalls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy?[0m
?[32m MergeAnnotatedRegions ?[31m(EXPERIMENTAL Tool) ?[36mMerge annotated genomic regions based entirely on touching/overlapping intervals.?[0m
?[32m MergeAnnotatedRegionsByAnnotation ?[31m(EXPERIMENTAL Tool) ?[36mMerge annotated genomic regions within specified distance if annotation value(s) are exactly the same.?[0m
?[32m ModelSegments ?[36mModels segmented copy ratios from denoised copy ratios and segmented minor-allele fractions from allelic counts?[0m
?[32m PlotDenoisedCopyRatios ?[36mCreates plots of denoised copy ratios?[0m
?[32m PlotModeledSegments ?[36mCreates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates?[0m
?[32m PostprocessGermlineCNVCalls ?[36mPostprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios?[0m
?[32m TagGermlineEvents ?[31m(EXPERIMENTAL Tool) ?[36mDo a simplistic tagging of germline events in a tumor segment file.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mCoverage Analysis: Tools that count coverage, e.g. depth per allele?[0m
?[32m ASEReadCounter ?[36mGenerates table of filtered base counts at het sites for allele specific expression?[0m
?[32m AnalyzeSaturationMutagenesis ?[31m(BETA Tool) ?[36m(EXPERIMENTAL) Processes reads from a MITESeq or other saturation mutagenesis experiment.?[0m
?[32m CallableLoci ?[31m(EXPERIMENTAL Tool) ?[36mDetermine callable status of loci?[0m
?[32m CollectAllelicCounts ?[36mCollects reference and alternate allele counts at specified sites?[0m
?[32m CollectAllelicCountsSpark ?[36mCollects reference and alternate allele counts at specified sites?[0m
?[32m CollectF1R2Counts ?[36mCollect F1R2 read counts for the Mutect2 orientation bias mixture model filter?[0m
?[32m CollectReadCounts ?[36mCollects read counts at specified intervals?[0m
?[32m CountBases ?[36mCount bases in a SAM/BAM/CRAM file?[0m
?[32m CountBasesSpark ?[36mCounts bases in the input SAM/BAM?[0m
?[32m CountReads ?[36mCount reads in a SAM/BAM/CRAM file?[0m
?[32m CountReadsSpark ?[36mCounts reads in the input SAM/BAM?[0m
?[32m DepthOfCoverage ?[31m(BETA Tool) ?[36mGenerate coverage summary information for reads data?[0m
?[32m GatherNormalArtifactData ?[36mCombine output files from GetNormalArtifactData in the order defined by a sequence dictionary?[0m
?[32m GeneExpressionEvaluation ?[31m(BETA Tool) ?[36mEvaluate gene expression from RNA-seq reads aligned to genome.?[0m
?[32m GetNormalArtifactData ?[36mCollects data for training normal artifact filter?[0m
?[32m GetPileupSummaries ?[36mTabulates pileup metrics for inferring contamination?[0m
?[32m LocalAssembler ?[31m(BETA Tool) ?[36mLocal assembler for SVs?[0m
?[32m Pileup ?[36mPrints read alignments in samtools pileup format?[0m
?[32m PileupSpark ?[31m(BETA Tool) ?[36mPrints read alignments in samtools pileup format?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics?[0m
?[32m AccumulateQualityYieldMetrics (Picard) ?[36mCombines multiple QualityYieldMetrics files into a single file.?[0m
?[32m AccumulateVariantCallingMetrics (Picard) ?[36mCombines multiple Variant Calling Metrics files into a single file?[0m
?[32m AnalyzeCovariates ?[36mEvaluate and compare base quality score recalibration (BQSR) tables?[0m
?[32m BamIndexStats (Picard) ?[36mGenerate index statistics from a BAM file?[0m
?[32m CalcMetadataSpark ?[31m(BETA Tool) ?[36m(Internal) Collects read metrics relevant to structural variant discovery?[0m
?[32m CalculateContamination ?[36mCalculate the fraction of reads coming from cross-sample contamination?[0m
?[32m CalculateFingerprintMetrics (Picard) ?[36mCalculate statistics on fingerprints, checking their viability?[0m
?[32m CalculateReadGroupChecksum (Picard) ?[36mCreates a hash code based on the read groups (RG). ?[0m
?[32m CheckDuplicateMarking (Picard) ?[36mChecks the consistency of duplicate markings.?[0m
?[32m CheckFingerprint (Picard) ?[36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes?[0m
?[32m CheckPileup ?[36mCompare GATK's internal pileup to a reference Samtools mpileup?[0m
?[32m CheckTerminatorBlock (Picard) ?[36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise?[0m
?[32m ClusterCrosscheckMetrics (Picard) ?[36mClusters the results of a CrosscheckFingerprints run by LOD score?[0m
?[32m CollectAlignmentSummaryMetrics (Picard) ?[36m<b>Produces a summary of alignment metrics from a SAM or BAM file.</b> ?[0m
?[32m CollectArraysVariantCallingMetrics (Picard) ?[36mCollects summary and per-sample from the provided arrays VCF file?[0m
?[32m CollectBaseDistributionByCycle (Picard) ?[36mChart the nucleotide distribution per cycle in a SAM or BAM file?[0m
?[32m CollectBaseDistributionByCycleSpark ?[31m(BETA Tool) ?[36mCollects base distribution per cycle in SAM/BAM/CRAM file(s).?[0m
?[32m CollectGcBiasMetrics (Picard) ?[36mCollect metrics regarding GC bias. ?[0m
?[32m CollectHiSeqXPfFailMetrics (Picard) ?[36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.?[0m
?[32m CollectHsMetrics (Picard) ?[36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. ?[0m
?[32m CollectIndependentReplicateMetrics (Picard) ?[31m(EXPERIMENTAL Tool) ?[36mEstimates the rate of independent replication rate of reads within a bam.
?[0m
?[32m CollectInsertSizeMetrics (Picard) ?[36mCollect metrics about the insert size distribution of a paired-end library. ?[0m
?[32m CollectInsertSizeMetricsSpark ?[31m(BETA Tool) ?[36mCollects insert size distribution information on alignment data?[0m
?[32m CollectJumpingLibraryMetrics (Picard) ?[36mCollect jumping library metrics. ?[0m
?[32m CollectMultipleMetrics (Picard) ?[36mCollect multiple classes of metrics. ?[0m
?[32m CollectMultipleMetricsSpark ?[31m(BETA Tool) ?[36mRuns multiple metrics collection modules for a given alignment file?[0m
?[32m CollectOxoGMetrics (Picard) ?[36mCollect metrics to assess oxidative artifacts.?[0m
?[32m CollectQualityYieldMetrics (Picard) ?[36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. ?[0m
?[32m CollectQualityYieldMetricsFlow (Picard) ?[31m(EXPERIMENTAL Tool) ?[36mCollect metrics about reads that pass quality thresholds from flow based read files. ?[0m
?[32m CollectQualityYieldMetricsSNVQ (Picard) ?[36mCollect SNVQ metrics about reads that pass quality thresholds and other filters (such as vendor fail, etc). ?[0m
?[32m CollectQualityYieldMetricsSpark ?[31m(BETA Tool) ?[36mCollects quality yield metrics from SAM/BAM/CRAM file(s).?[0m
?[32m CollectRawWgsMetrics (Picard) ?[36mCollect whole genome sequencing-related metrics. ?[0m
?[32m CollectRnaSeqMetrics (Picard) ?[36mProduces RNA alignment metrics for a SAM or BAM file. ?[0m
?[32m CollectRrbsMetrics (Picard) ?[36m<b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b> ?[0m
?[32m CollectSamErrorMetrics (Picard) ?[36mProgram to collect error metrics on bases stratified in various ways.?[0m
?[32m CollectSequencingArtifactMetrics (Picard) ?[36mCollect metrics to quantify single-base sequencing artifacts. ?[0m
?[32m CollectTargetedPcrMetrics (Picard) ?[36mCalculate PCR-related metrics from targeted sequencing data. ?[0m
?[32m CollectVariantCallingMetrics (Picard) ?[36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file?[0m
?[32m CollectWgsMetrics (Picard) ?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.?[0m
?[32m CollectWgsMetricsWithNonZeroCoverage (Picard)?[31m(EXPERIMENTAL Tool) ?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. ?[0m
?[32m CompareBaseQualities ?[36mCompares the base qualities of two SAM/BAM/CRAM files?[0m
?[32m CompareDuplicatesSpark ?[31m(BETA Tool) ?[36mDetermine if two potentially identical BAMs have the same duplicate reads?[0m
?[32m CompareMetrics (Picard) ?[36mCompare two metrics files.?[0m
?[32m CompareSAMs (Picard) ?[36mCompare two input SAM/BAM/CRAM files. ?[0m
?[32m ConvertHaplotypeDatabaseToVcf (Picard) ?[36mConvert Haplotype database file to vcf?[0m
?[32m ConvertSequencingArtifactToOxoG (Picard) ?[36mExtract OxoG metrics from generalized artifacts metrics. ?[0m
?[32m CrosscheckFingerprints (Picard) ?[36mChecks that all data in the input files appear to have come from the same individual?[0m
?[32m CrosscheckReadGroupFingerprints (Picard) ?[36mDEPRECATED: USE CrosscheckFingerprints. ?[0m
?[32m DumpTabixIndex ?[36mDumps a tabix index file.?[0m
?[32m EstimateLibraryComplexity (Picard) ?[36mEstimates the numbers of unique molecules in a sequencing library. ?[0m
?[32m ExtractFingerprint (Picard) ?[36mComputes a fingerprint from the input file.?[0m
?[32m FlagStat ?[36mAccumulate flag statistics given a BAM file?[0m
?[32m FlagStatSpark ?[36mSpark tool to accumulate flag statistics?[0m
?[32m GatherPileupSummaries ?[36mCombine output files from GetPileupSummary in the order defined by a sequence dictionary?[0m
?[32m GetSampleName ?[36mEmit a single sample name?[0m
?[32m IdentifyContaminant (Picard) ?[36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.?[0m
?[32m LiftOverHaplotypeMap (Picard) ?[36mLifts over a haplotype database from one reference to another?[0m
?[32m MeanQualityByCycle (Picard) ?[36mCollect mean quality by cycle.?[0m
?[32m MeanQualityByCycleSpark ?[31m(BETA Tool) ?[36mMeanQualityByCycle on Spark?[0m
?[32m QualityScoreDistribution (Picard) ?[36mChart the distribution of quality scores. ?[0m
?[32m QualityScoreDistributionSpark ?[31m(BETA Tool) ?[36mQualityScoreDistribution on Spark?[0m
?[32m ValidateSamFile (Picard) ?[36mValidates a SAM/BAM/CRAM file.?[0m
?[32m ViewSam (Picard) ?[36mPrints a SAM or BAM file to the screen?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mExample Tools: Example tools that show developers how to implement new tools?[0m
?[32m ExampleMultiFeatureWalker ?[36mExample of a MultiFeatureWalker subclass.?[0m
?[32m HtsgetReader ?[31m(EXPERIMENTAL Tool) ?[36mDownload a file using htsget?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mFlow Based Tools: Tools designed specifically to operate on flow based data?[0m
?[32m AddFlowBaseQuality ?[31m(EXPERIMENTAL Tool) ?[36mAdd base quality attribute to reads in in the SAM/BAM/CRAM file?[0m
?[32m AddFlowSNVQuality ?[31m(EXPERIMENTAL Tool) ?[36mAdd SNV Quality to the flow-based CRAM?[0m
?[32m CalculateAverageCombinedAnnotations ?[31m(EXPERIMENTAL Tool) ?[36mDivides annotations that were summed by genomicsDB by number of samples to calculate average.?[0m
?[32m FlowFeatureMapper ?[31m(EXPERIMENTAL Tool) ?[36mMap/find features in BAM file, output VCF. Initially mapping SNVs?[0m
?[32m FlowPairHMMAlignReadsToHaplotypes ?[31m(EXPERIMENTAL Tool) ?[36mProduces readxhaplotype matrix with likelihoods of read / haplotype?[0m
?[32m GroundTruthReadsBuilder ?[31m(EXPERIMENTAL Tool) ?[36mProduces a flexible and robust ground truth set for base calling training?[0m
?[32m GroundTruthScorer ?[31m(EXPERIMENTAL Tool) ?[36mScore reads against a reference/ground truth?[0m
?[32m SplitCRAM ?[31m(EXPERIMENTAL Tool) ?[36mSplit CRAM files to smaller files efficiently?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays?[0m
?[32m BpmToNormalizationManifestCsv (Picard) ?[36mProgram to convert an Illumina bpm file into a bpm.csv file.?[0m
?[32m CombineGenotypingArrayVcfs (Picard) ?[36mProgram to combine multiple genotyping array VCF files into one VCF.?[0m
?[32m CompareGtcFiles (Picard) ?[36mCompares two GTC files.?[0m
?[32m CreateBafRegressMetricsFile (Picard) ?[36mProgram to generate a picard metrics file from the output of the bafRegress tool.?[0m
?[32m CreateExtendedIlluminaManifest (Picard) ?[36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf?[0m
?[32m CreateVerifyIDIntensityContaminationMetricsFile (Picard) ?[36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.?[0m
?[32m GtcToVcf (Picard) ?[36mProgram to convert an Illumina GTC file to a VCF?[0m
?[32m MergePedIntoVcf (Picard) ?[36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.?[0m
?[32m VcfToAdpc (Picard) ?[36mProgram to convert an Arrays VCF to an ADPC file.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mIntervals Manipulation: Tools that process genomic intervals in various formats?[0m
?[32m BedToIntervalList (Picard) ?[36mConverts a BED file to a Picard Interval List. ?[0m
?[32m CompareIntervalLists ?[36mCompare two interval lists for equality?[0m
?[32m IntervalListToBed (Picard) ?[36mConverts an Picard IntervalList file to a BED file.?[0m
?[32m IntervalListTools (Picard) ?[36mA tool for performing various IntervalList manipulations?[0m
?[32m LiftOverIntervalList (Picard) ?[36mLifts over an interval list from one reference build to another. ?[0m
?[32m PreprocessIntervals ?[36mPrepares bins for coverage collection?[0m
?[32m SplitIntervals ?[36mSplit intervals into sub-interval files.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mMetagenomics: Tools that perform metagenomic analysis, e.g. microbial community composition and pathogen detection?[0m
?[32m PathSeqBuildKmers ?[36mBuilds set of host reference k-mers?[0m
?[32m PathSeqBuildReferenceTaxonomy ?[36mBuilds a taxonomy datafile of the microbe reference?[0m
?[32m PathSeqBwaSpark ?[36mStep 2: Aligns reads to the microbe reference?[0m
?[32m PathSeqFilterSpark ?[36mStep 1: Filters low quality, low complexity, duplicate, and host reads?[0m
?[32m PathSeqPipelineSpark ?[36mCombined tool that performs all steps: read filtering, microbe reference alignment, and abundance scoring?[0m
?[32m PathSeqScoreSpark ?[36mStep 3: Classifies pathogen-aligned reads and generates abundance scores?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mMethylation-Specific Tools: Tools that perform methylation calling, processing bisulfite sequenced, methylation-aware aligned BAM?[0m
?[32m MethylationTypeCaller ?[31m(EXPERIMENTAL Tool) ?[36mIdentify methylated bases from bisulfite sequenced, methylation-aware BAMs?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mOther: Miscellaneous tools, e.g. those that aid in data streaming?[0m
?[32m CRAMIssue8768Detector ?[31m(EXPERIMENTAL Tool) ?[36mAnalyze a CRAM file to check for base corruption caused by GATK issue 8768?[0m
?[32m CreateHadoopBamSplittingIndex ?[31m(BETA Tool) ?[36mCreate a Hadoop BAM splitting index?[0m
?[32m FifoBuffer (Picard) ?[36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.?[0m
?[32m GatherBQSRReports ?[36mGathers scattered BQSR recalibration reports into a single file?[0m
?[32m GatherTranches ?[31m(BETA Tool) ?[36mGathers scattered VQSLOD tranches into a single file?[0m
?[32m IndexFeatureFile ?[36mCreates an index for a feature file, e.g. VCF or BED file.?[0m
?[32m ParallelCopyGCSDirectoryIntoHDFSSpark ?[31m(BETA Tool) ?[36mParallel copy a file or directory from Google Cloud Storage into the HDFS file system used by Spark?[0m
?[32m PrintBGZFBlockInformation ?[31m(EXPERIMENTAL Tool) ?[36mPrint information about the compressed blocks in a BGZF format file?[0m
?[32m PrintFileDiagnostics ?[31m(EXPERIMENTAL Tool) ?[36mPrint diagnostic information about a genomics file to stdout?[0m
?[32m ReadAnonymizer ?[31m(EXPERIMENTAL Tool) ?[36mReplace bases in reads with reference bases.?[0m
?[32m ReblockGVCF ?[36mCondenses homRef blocks in a single-sample GVCF?[0m
?[32m SortGff (Picard) ?[36mSorts a gff3 file, and adds flush directives?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mRead Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format?[0m
?[32m AddCommentsToBam (Picard) ?[36mAdds comments to the header of a BAM file.?[0m
?[32m AddOATag (Picard) ?[36mRecord current alignment information to OA tag.?[0m
?[32m AddOrReplaceReadGroups (Picard) ?[36mAssigns all the reads in a file to a single new read-group.?[0m
?[32m AddOriginalAlignmentTags ?[31m(EXPERIMENTAL Tool) ?[36mAdds Original Alignment tag and original mate contig tag?[0m
?[32m ApplyBQSR ?[36mApply base quality score recalibration?[0m
?[32m ApplyBQSRSpark ?[31m(BETA Tool) ?[36mApply base quality score recalibration on Spark?[0m
?[32m BQSRPipelineSpark ?[31m(BETA Tool) ?[36mBoth steps of BQSR (BaseRecalibrator and ApplyBQSR) on Spark?[0m
?[32m BamToBfq (Picard) ?[36mConverts a BAM file into a BFQ (binary fastq formatted) file?[0m
?[32m BaseRecalibrator ?[36mGenerates recalibration table for Base Quality Score Recalibration (BQSR)?[0m
?[32m BaseRecalibratorSpark ?[31m(BETA Tool) ?[36mGenerate recalibration table for Base Quality Score Recalibration (BQSR) on Spark?[0m
?[32m BuildBamIndex (Picard) ?[36mGenerates a BAM index ".bai" file. ?[0m
?[32m BwaAndMarkDuplicatesPipelineSpark ?[31m(BETA Tool) ?[36mTakes name-sorted file and runs BWA and MarkDuplicates.?[0m
?[32m BwaSpark ?[31m(BETA Tool) ?[36mAlign reads to a given reference using BWA on Spark?[0m
?[32m CleanSam (Picard) ?[36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads?[0m
?[32m ClipReads ?[36mClip reads in a SAM/BAM/CRAM file?[0m
?[32m CollectDuplicateMetrics (Picard) ?[36mCollect Duplicate metrics from marked file.?[0m
?[32m ConvertHeaderlessHadoopBamShardToBam ?[31m(BETA Tool) ?[36mConvert a headerless BAM shard into a readable BAM?[0m
?[32m DownsampleByDuplicateSet ?[31m(BETA Tool) ?[36mDiscard a set fraction of duplicate sets from a UMI-grouped bam?[0m
?[32m DownsampleSam (Picard) ?[36mDownsample a SAM or BAM file.?[0m
?[32m ExtractOriginalAlignmentRecordsByNameSpark ?[31m(BETA Tool) ?[36mSubsets reads by name?[0m
?[32m FastqToSam (Picard) ?[36mConverts a FASTQ file to an unaligned BAM or SAM file?[0m
?[32m FilterSamReads (Picard) ?[36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.?[0m
?[32m FixMateInformation (Picard) ?[36mVerify mate-pair information between mates and fix if needed.?[0m
?[32m FixMisencodedBaseQualityReads ?[36mFix Illumina base quality scores in a SAM/BAM/CRAM file?[0m
?[32m GatherBamFiles (Picard) ?[36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis?[0m
?[32m LeftAlignIndels ?[36mLeft-aligns indels from reads in a SAM/BAM/CRAM file?[0m
?[32m MarkDuplicates (Picard) ?[36mIdentifies duplicate reads. ?[0m
?[32m MarkDuplicatesSpark ?[36mMarkDuplicates on Spark?[0m
?[32m MarkDuplicatesWithMateCigar (Picard) ?[36mIdentifies duplicate reads, accounting for mate CIGAR. ?[0m
?[32m MergeBamAlignment (Picard) ?[36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. ?[0m
?[32m MergeSamFiles (Picard) ?[36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. ?[0m
?[32m PositionBasedDownsampleSam (Picard) ?[36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.?[0m
?[32m PostProcessReadsForRSEM ?[31m(BETA Tool) ?[36mReorder reads before running RSEM?[0m
?[32m PrintDistantMates ?[36mUnmaps reads with distant mates.?[0m
?[32m PrintReads ?[36mPrint reads in the SAM/BAM/CRAM file?[0m
?[32m PrintReadsHeader ?[36mPrint the header from a SAM/BAM/CRAM file?[0m
?[32m PrintReadsSpark ?[36mPrintReads on Spark?[0m
?[32m ReorderSam (Picard) ?[36mReorders reads in a SAM or BAM file to match ordering in a second reference file.?[0m
?[32m ReplaceSamHeader (Picard) ?[36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. ?[0m
?[32m RevertBaseQualityScores ?[36mRevert Quality Scores in a SAM/BAM/CRAM file?[0m
?[32m RevertOriginalBaseQualitiesAndAddMateCigar (Picard)?[36mReverts the original base qualities and adds the mate cigar tag to read-group files?[0m
?[32m RevertSam (Picard) ?[36mReverts SAM/BAM/CRAM files to a previous state. ?[0m
?[32m RevertSamSpark ?[31m(BETA Tool) ?[36mReverts SAM, BAM or CRAM files to a previous state.?[0m
?[32m SamFormatConverter (Picard) ?[36mConvert a BAM file to a SAM file, or a SAM to a BAM?[0m
?[32m SamToFastq (Picard) ?[36mConverts a SAM/BAM/CRAM file to FASTQ.?[0m
?[32m SamToFastqWithTags (Picard) ?[36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.?[0m
?[32m SetNmAndUqTags (Picard) ?[36mDEPRECATED: Use SetNmMdAndUqTags instead.?[0m
?[32m SetNmMdAndUqTags (Picard) ?[36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file ?[0m
?[32m SimpleMarkDuplicatesWithMateCigar (Picard) ?[31m(EXPERIMENTAL Tool) ?[36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.?[0m
?[32m SortSam (Picard) ?[36mSorts a SAM, BAM or CRAM file. ?[0m
?[32m SortSamSpark ?[31m(BETA Tool) ?[36mSortSam on Spark (works on SAM/BAM/CRAM)?[0m
?[32m SplitNCigarReads ?[36mSplit Reads with N in Cigar?[0m
?[32m SplitReads ?[36mOutputs reads from a SAM/BAM/CRAM by read group, sample and library name?[0m
?[32m SplitSamByLibrary (Picard) ?[36mSplits a SAM/BAM/CRAM file into individual files by library?[0m
?[32m SplitSamByNumberOfReads (Picard) ?[36mSplits a SAM/BAM/CRAM file to multiple files.?[0m
?[32m TransferReadTags ?[31m(EXPERIMENTAL Tool) ?[36mIncorporate read tags in a SAM file to that of a matching SAM file?[0m
?[32m UmiAwareMarkDuplicatesWithMateCigar (Picard) ?[31m(EXPERIMENTAL Tool) ?[36mIdentifies duplicate reads using information from read positions and UMIs. ?[0m
?[32m UnmarkDuplicates ?[36mClears the 0x400 duplicate SAM flag?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mReference: Tools that analyze and manipulate FASTA format references?[0m
?[32m BaitDesigner (Picard) ?[36mDesigns oligonucleotide baits for hybrid selection reactions.?[0m
?[32m BwaMemIndexImageCreator ?[36mCreate a BWA-MEM index image file for use with GATK BWA tools?[0m
?[32m CheckReferenceCompatibility ?[31m(EXPERIMENTAL Tool) ?[36mCheck a BAM/VCF for compatibility against specified references.?[0m
?[32m CompareReferences ?[31m(EXPERIMENTAL Tool) ?[36mDisplay reference comparison as a tab-delimited table and summarize reference differences.?[0m
?[32m ComposeSTRTableFile ?[36mComposes a genome-wide STR location table used for DragSTR model auto-calibration?[0m
?[32m CountBasesInReference ?[36mCount the numbers of each base in a reference file?[0m
?[32m CreateSequenceDictionary (Picard) ?[36mCreates a sequence dictionary for a reference sequence. ?[0m
?[32m ExtractSequences (Picard) ?[36mSubsets intervals from a reference sequence to a new FASTA file.?[0m
?[32m FastaAlternateReferenceMaker ?[36mCreate an alternative reference by combining a fasta with a vcf.?[0m
?[32m FastaReferenceMaker ?[36mCreate snippets of a fasta file?[0m
?[32m FindBadGenomicKmersSpark ?[31m(BETA Tool) ?[36mIdentifies sequences that occur at high frequency in a reference?[0m
?[32m NonNFastaSize (Picard) ?[36mCounts the number of non-N bases in a fasta file.?[0m
?[32m NormalizeFasta (Picard) ?[36mNormalizes lines of sequence in a FASTA file to be of the same length.?[0m
?[32m ScatterIntervalsByNs (Picard) ?[36mWrites an interval list created by splitting a reference at Ns.?[0m
?[32m ShiftFasta ?[31m(BETA Tool) ?[36mCreates a shifted fasta file and shift_back file?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mShort Variant Discovery: Tools that perform variant calling and genotyping for short variants (SNPs, SNVs and Indels)?[0m
?[32m CalibrateDragstrModel ?[36mestimates the parameters for the DRAGstr model?[0m
?[32m CombineGVCFs ?[36mMerges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations?[0m
?[32m GenomicsDBImport ?[36mImport VCFs to GenomicsDB?[0m
?[32m GenotypeGVCFs ?[36mPerform joint genotyping on one or more samples pre-called with HaplotypeCaller?[0m
?[32m GnarlyGenotyper ?[31m(BETA Tool) ?[36mPerform "quick and dirty" joint genotyping on one or more samples pre-called with HaplotypeCaller?[0m
?[32m GtfToBed ?[36mGencode GTF to BED?[0m
?[32m HaplotypeBasedVariantRecaller ?[31m(EXPERIMENTAL Tool) ?[36mCalculate likelihood matrix for each Allele in VCF against a set of Reads limited by a set of Haplotypes?[0m
?[32m HaplotypeCaller ?[36mCall germline SNPs and indels via local re-assembly of haplotypes?[0m
?[32m HaplotypeCallerSpark ?[31m(BETA Tool) ?[36mHaplotypeCaller on Spark?[0m
?[32m LearnReadOrientationModel ?[36mGet the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter?[0m
?[32m MergeMutectStats ?[36mMerge the stats output by scatters of a single Mutect2 job?[0m
?[32m Mutect2 ?[36mCall somatic SNVs and indels via local assembly of haplotypes?[0m
?[32m RampedHaplotypeCaller ?[31m(EXPERIMENTAL Tool) ?[36mCall germline SNPs and indels via local re-assembly of haplotypes (ramped version)?[0m
?[32m ReadsPipelineSpark ?[31m(BETA Tool) ?[36mRuns BWA (if specified), MarkDuplicates, BQSR, and HaplotypeCaller on unaligned or aligned reads to generate a VCF.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mStructural Variant Discovery: Tools that detect structural variants ?[0m
?[32m CollectSVEvidence ?[31m(BETA Tool) ?[36mGathers paired-end and split read evidence files for use in the GATK-SV pipeline.?[0m
?[32m CondenseDepthEvidence ?[31m(EXPERIMENTAL Tool) ?[36mMerges adjacent DepthEvidence records.?[0m
?[32m CpxVariantReInterpreterSpark ?[31m(BETA Tool) ?[36m(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf?[0m
?[32m DiscoverVariantsFromContigAlignmentsSAMSpark ?[31m(BETA Tool) ?[36m(Internal) Examines aligned contigs from local assemblies and calls structural variants?[0m
?[32m ExtractSVEvidenceSpark ?[31m(BETA Tool) ?[36m(Internal) Extracts evidence of structural variations from reads?[0m
?[32m FindBreakpointEvidenceSpark ?[31m(BETA Tool) ?[36m(Internal) Produces local assemblies of genomic regions that may harbor structural variants?[0m
?[32m GroupedSVCluster ?[31m(BETA Tool) ?[36mClusters structural variants grouping by type, size, and track overlap?[0m
?[32m JointGermlineCNVSegmentation ?[31m(BETA Tool) ?[36mCombine segmented gCNV VCFs.?[0m
?[32m PrintReadCounts ?[31m(EXPERIMENTAL Tool) ?[36mPrints count files for CNV determination.?[0m
?[32m PrintSVEvidence ?[31m(EXPERIMENTAL Tool) ?[36mMerges SV evidence records.?[0m
?[32m SVAnnotate ?[36mAdds gene overlap and variant consequence annotations to SV VCF from GATK-SV pipeline?[0m
?[32m SVCluster ?[31m(BETA Tool) ?[36mClusters structural variants?[0m
?[32m SVConcordance ?[31m(BETA Tool) ?[36mAnnotates structural variant genotype concordance?[0m
?[32m SVStratify ?[31m(BETA Tool) ?[36mAnnotates variants by SV type, size, and reference tracks?[0m
?[32m SiteDepthtoBAF ?[31m(EXPERIMENTAL Tool) ?[36mConvert SiteDepth to BafEvidence?[0m
?[32m StructuralVariantDiscoverer ?[31m(BETA Tool) ?[36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints?[0m
?[32m StructuralVariationDiscoveryPipelineSpark ?[31m(BETA Tool) ?[36mRuns the structural variation discovery workflow on a single sample?[0m
?[32m SvDiscoverFromLocalAssemblyContigAlignmentsSpark ?[31m(BETA Tool) ?[36m(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mTest Tools: Tools for internal test purposes ?[0m
?[32m DummyGatkTool ?[36mempty class?[0m
?[32m DummyPlaceholderGatkTool ?[36mDummy dumb dumb tool for testing.?[0m
?[32m DummySparkToolRequiresReference ?[36mempty class?[0m
?[32m TestGATKSparkToolWithVariants ?[36mTestGATKSparkToolWithVariants?[0m
?[32m VariantEmitter ?[36mTest tool?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine?[0m
?[32m AlleleFrequencyQC ?[31m(BETA Tool) ?[36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)?[0m
?[32m AnnotateVcfWithBamDepth ?[36m(Internal) Annotate a vcf with a bam's read depth at each variant locus?[0m
?[32m AnnotateVcfWithExpectedAlleleFraction ?[36m(Internal) Annotate a vcf with expected allele fractions in pooled sequencing?[0m
?[32m CalculateGenotypePosteriors ?[36mCalculate genotype posterior probabilities given family and/or known population genotypes?[0m
?[32m CalculateMixingFractions ?[36m(Internal) Calculate proportions of different samples in a pooled bam?[0m
?[32m Concordance ?[36mEvaluate concordance of an input VCF against a validated truth VCF?[0m
?[32m CountFalsePositives ?[31m(BETA Tool) ?[36mCount PASS variants?[0m
?[32m CountVariants ?[36mCounts variant records in a VCF file, regardless of filter status.?[0m
?[32m CountVariantsSpark ?[36mCountVariants on Spark?[0m
?[32m EvaluateInfoFieldConcordance ?[31m(BETA Tool) ?[36mEvaluate concordance of info fields in an input VCF against a validated truth VCF?[0m
?[32m FilterFuncotations ?[31m(EXPERIMENTAL Tool) ?[36mFilter variants based on clinically-significant Funcotations.?[0m
?[32m FindMendelianViolations (Picard) ?[36mFinds mendelian violations of all types within a VCF?[0m
?[32m FuncotateSegments ?[31m(BETA Tool) ?[36mFunctional annotation for segment files. The output formats are not well-defined and subject to change.?[0m
?[32m Funcotator ?[36mFunctional Annotator?[0m
?[32m FuncotatorDataSourceDownloader ?[36mData source downloader for Funcotator.?[0m
?[32m GenotypeConcordance (Picard) ?[36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.?[0m
?[32m MergeMutect2CallsWithMC3 ?[31m(EXPERIMENTAL Tool) ?[36mUNSUPPORTED. FOR EVALUATION ONLY. Merge M2 calls with MC?[0m
?[32m ReferenceBlockConcordance ?[36mEvaluate GVCF reference block concordance of an input GVCF against a truth GVCF?[0m
?[32m VCFComparator ?[31m(EXPERIMENTAL Tool) ?[36mCompare two VCFs?[0m
?[32m ValidateBasicSomaticShortMutations ?[31m(EXPERIMENTAL Tool) ?[36mCheck variants against tumor-normal bams representing the same samples, though not the ones from the actual calls.?[0m
?[32m ValidateVariants ?[36mValidate VCF?[0m
?[32m VariantEval ?[31m(BETA Tool) ?[36mGeneral-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)?[0m
?[32m VariantsToTable ?[36mExtract fields from a VCF file to a tab-delimited table?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Filtering: Tools that filter variants by annotating the FILTER column?[0m
?[32m ApplyVQSR ?[36m Apply a score cutoff to filter variants based on a recalibration table?[0m
?[32m CreateSomaticPanelOfNormals ?[31m(BETA Tool) ?[36mMake a panel of normals for use with Mutect2?[0m
?[32m ExtractVariantAnnotations ?[31m(BETA Tool) ?[36mExtracts site-level variant annotations, labels, and other metadata from a VCF file to HDF5 files?[0m
?[32m FilterAlignmentArtifacts ?[31m(EXPERIMENTAL Tool) ?[36mFilter alignment artifacts from a vcf callset.?[0m
?[32m FilterMutectCalls ?[36mFilter somatic SNVs and indels called by Mutect2?[0m
?[32m FilterVariantTranches ?[36mApply tranche filtering?[0m
?[32m FilterVcf (Picard) ?[36mHard filters a VCF.?[0m
?[32m MTLowHeteroplasmyFilterTool ?[36mIf too many low het sites, filter all low het sites?[0m
?[32m NVScoreVariants ?[31m(BETA Tool) ?[36mAnnotate a VCF with scores from a PyTorch-based Convolutional Neural Network (CNN)?[0m
?[32m NuMTFilterTool ?[36mUses the median autosomal coverage and the allele depth to determine whether the allele might be a NuMT?[0m
?[32m ScoreVariantAnnotations ?[31m(BETA Tool) ?[36mScores variant calls in a VCF file based on site-level annotations using a previously trained model?[0m
?[32m TrainVariantAnnotationsModel ?[31m(BETA Tool) ?[36mTrains a model for scoring variant calls based on site-level annotations?[0m
?[32m VariantFiltration ?[36mFilter variant calls based on INFO and/or FORMAT annotations?[0m
?[32m VariantRecalibrator ?[36mBuild a recalibration model to score variant quality for filtering purposes?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data?[0m
?[32m FixVcfHeader (Picard) ?[36mReplaces or fixes a VCF header.?[0m
?[32m GatherVcfs (Picard) ?[36mGathers multiple VCF files from a scatter operation into a single VCF file?[0m
?[32m GatherVcfsCloud ?[36mGathers multiple VCF files from a scatter operation into a single VCF file?[0m
?[32m LeftAlignAndTrimVariants ?[36mLeft align and trim vairants?[0m
?[32m LiftoverVcf (Picard) ?[36mLifts over a VCF file from one reference build to another. ?[0m
?[32m MakeSitesOnlyVcf (Picard) ?[36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.?[0m
?[32m MakeVcfSampleNameMap (Picard) ?[36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.?[0m
?[32m MergeVcfs (Picard) ?[36mCombines multiple variant files into a single variant file?[0m
?[32m PrintVariantsSpark ?[36mPrints out variants from the input VCF.?[0m
?[32m RemoveNearbyIndels ?[36m(Internal) Remove indels from the VCF file that are close to each other.?[0m
?[32m RenameSampleInVcf (Picard) ?[36mRenames a sample within a VCF or BCF.?[0m
?[32m SelectVariants ?[36mSelect a subset of variants from a VCF file?[0m
?[32m SortVcf (Picard) ?[36mSorts one or more VCF files. ?[0m
?[32m SplitVcfs (Picard) ?[36mSplits SNPs and INDELs into separate files. ?[0m
?[32m UpdateVCFSequenceDictionary ?[36mUpdates the sequence dictionary in a variant file.?[0m
?[32m UpdateVcfSequenceDictionary (Picard) ?[36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.?[0m
?[32m VariantAnnotator ?[36mTool for adding annotations to VCF files?[0m
?[32m VcfFormatConverter (Picard) ?[36mConverts VCF to BCF or BCF to VCF. ?[0m
?[32m VcfToIntervalList (Picard) ?[36mConverts a VCF or BCF file to a Picard Interval List?[0m
?[37m--------------------------------------------------------------------------------------
?[0m