?[1m?[31mUSAGE: PicardCommandLine ?[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 ?[31m?[36mAsserts the validity for specified Illumina basecalling data. ?[0m
?[32m CollectIlluminaBasecallingMetrics ?[31m?[36mCollects Illumina Basecalling metrics for a sequencing run. ?[0m
?[32m CollectIlluminaLaneMetrics ?[31m?[36mCollects Illumina lane metrics for the given BaseCalling analysis directory.?[0m
?[32m ExtractIlluminaBarcodes ?[31m?[36mTool determines the barcode for each read in an Illumina lane. ?[0m
?[32m IlluminaBasecallsToFastq ?[31m?[36mGenerate FASTQ file(s) from Illumina basecall read data. ?[0m
?[32m IlluminaBasecallsToSam ?[31m?[36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.?[0m
?[32m MarkIlluminaAdapters ?[31m?[36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics?[0m
?[32m AccumulateQualityYieldMetrics ?[31m?[36mCombines multiple QualityYieldMetrics files into a single file.?[0m
?[32m AccumulateVariantCallingMetrics ?[31m?[36mCombines multiple Variant Calling Metrics files into a single file?[0m
?[32m BamIndexStats ?[31m?[36mGenerate index statistics from a BAM file?[0m
?[32m CalculateFingerprintMetrics ?[31m?[36mCalculate statistics on fingerprints, checking their viability?[0m
?[32m CalculateReadGroupChecksum ?[31m?[36mCreates a hash code based on the read groups (RG). ?[0m
?[32m CheckDuplicateMarking ?[31m?[36mChecks the consistency of duplicate markings.?[0m
?[32m CheckFingerprint ?[31m?[36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes?[0m
?[32m CheckTerminatorBlock ?[31m?[36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise?[0m
?[32m ClusterCrosscheckMetrics ?[31m?[36mClusters the results of a CrosscheckFingerprints run by LOD score?[0m
?[32m CollectAlignmentSummaryMetrics ?[31m?[36m<b>Produces a summary of alignment metrics from a SAM or BAM file.</b> ?[0m
?[32m CollectArraysVariantCallingMetrics ?[31m?[36mCollects summary and per-sample from the provided arrays VCF file?[0m
?[32m CollectBaseDistributionByCycle ?[31m?[36mChart the nucleotide distribution per cycle in a SAM or BAM file?[0m
?[32m CollectGcBiasMetrics ?[31m?[36mCollect metrics regarding GC bias. ?[0m
?[32m CollectHiSeqXPfFailMetrics ?[31m?[36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.?[0m
?[32m CollectHsMetrics ?[31m?[36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. ?[0m
?[32m CollectIndependentReplicateMetrics ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mEstimates the rate of independent replication rate of reads within a bam.
?[0m
?[32m CollectInsertSizeMetrics ?[31m?[36mCollect metrics about the insert size distribution of a paired-end library. ?[0m
?[32m CollectJumpingLibraryMetrics ?[31m?[36mCollect jumping library metrics. ?[0m
?[32m CollectMultipleMetrics ?[31m?[36mCollect multiple classes of metrics. ?[0m
?[32m CollectOxoGMetrics ?[31m?[36mCollect metrics to assess oxidative artifacts.?[0m
?[32m CollectQualityYieldMetrics ?[31m?[36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. ?[0m
?[32m CollectQualityYieldMetricsFlow ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mCollect metrics about reads that pass quality thresholds from flow based read files. ?[0m
?[32m CollectQualityYieldMetricsSNVQ ?[31m?[36mCollect SNVQ metrics about reads that pass quality thresholds and other filters (such as vendor fail, etc). ?[0m
?[32m CollectRawWgsMetrics ?[31m?[36mCollect whole genome sequencing-related metrics. ?[0m
?[32m CollectRnaSeqMetrics ?[31m?[36mProduces RNA alignment metrics for a SAM or BAM file. ?[0m
?[32m CollectRrbsMetrics ?[31m?[36m<b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b> ?[0m
?[32m CollectSamErrorMetrics ?[31m?[36mProgram to collect error metrics on bases stratified in various ways.?[0m
?[32m CollectSequencingArtifactMetrics ?[31m?[36mCollect metrics to quantify single-base sequencing artifacts. ?[0m
?[32m CollectTargetedPcrMetrics ?[31m?[36mCalculate PCR-related metrics from targeted sequencing data. ?[0m
?[32m CollectUmiPrevalenceMetrics ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mTally the counts of UMIs in duplicate sets within a bam.
?[0m
?[32m CollectVariantCallingMetrics ?[31m?[36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file?[0m
?[32m CollectWgsMetrics ?[31m?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.?[0m
?[32m CollectWgsMetricsWithNonZeroCoverage ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. ?[0m
?[32m CompareMetrics ?[31m?[36mCompare two metrics files.?[0m
?[32m CompareSAMs ?[31m?[36mCompare two input SAM/BAM/CRAM files. ?[0m
?[32m ConvertHaplotypeDatabaseToVcf ?[31m?[36mConvert Haplotype database file to vcf?[0m
?[32m ConvertSequencingArtifactToOxoG ?[31m?[36mExtract OxoG metrics from generalized artifacts metrics. ?[0m
?[32m CrosscheckFingerprints ?[31m?[36mChecks that all data in the input files appear to have come from the same individual?[0m
?[32m CrosscheckReadGroupFingerprints ?[31m?[36mDEPRECATED: USE CrosscheckFingerprints. ?[0m
?[32m EstimateLibraryComplexity ?[31m?[36mEstimates the numbers of unique molecules in a sequencing library. ?[0m
?[32m ExtractFingerprint ?[31m?[36mComputes a fingerprint from the input file.?[0m
?[32m IdentifyContaminant ?[31m?[36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.?[0m
?[32m LiftOverHaplotypeMap ?[31m?[36mLifts over a haplotype database from one reference to another?[0m
?[32m MeanQualityByCycle ?[31m?[36mCollect mean quality by cycle.?[0m
?[32m QualityScoreDistribution ?[31m?[36mChart the distribution of quality scores. ?[0m
?[32m ValidateSamFile ?[31m?[36mValidates a SAM/BAM/CRAM file.?[0m
?[32m ViewSam ?[31m?[36mPrints a SAM or BAM file to the screen?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays?[0m
?[32m BpmToNormalizationManifestCsv ?[31m?[36mProgram to convert an Illumina bpm file into a bpm.csv file.?[0m
?[32m CombineGenotypingArrayVcfs ?[31m?[36mProgram to combine multiple genotyping array VCF files into one VCF.?[0m
?[32m CompareGtcFiles ?[31m?[36mCompares two GTC files.?[0m
?[32m CreateBafRegressMetricsFile ?[31m?[36mProgram to generate a picard metrics file from the output of the bafRegress tool.?[0m
?[32m CreateExtendedIlluminaManifest ?[31m?[36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf?[0m
?[32m CreateVerifyIDIntensityContaminationMetricsFile ?[31m?[36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.?[0m
?[32m GtcToVcf ?[31m?[36mProgram to convert an Illumina GTC file to a VCF?[0m
?[32m MergePedIntoVcf ?[31m?[36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.?[0m
?[32m VcfToAdpc ?[31m?[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 ?[31m?[36mConverts a BED file to a Picard Interval List. ?[0m
?[32m IntervalListToBed ?[31m?[36mConverts an Picard IntervalList file to a BED file.?[0m
?[32m IntervalListTools ?[31m?[36mA tool for performing various IntervalList manipulations?[0m
?[32m LiftOverIntervalList ?[31m?[36mLifts over an interval list from one reference build to another. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mOther: Miscellaneous tools, e.g. those that aid in data streaming?[0m
?[32m FifoBuffer ?[31m?[36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.?[0m
?[32m SortGff ?[31m?[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 ?[31m?[36mAdds comments to the header of a BAM file.?[0m
?[32m AddOATag ?[31m?[36mRecord current alignment information to OA tag.?[0m
?[32m AddOrReplaceReadGroups ?[31m?[36mAssigns all the reads in a file to a single new read-group.?[0m
?[32m BamToBfq ?[31m?[36mConverts a BAM file into a BFQ (binary fastq formatted) file?[0m
?[32m BuildBamIndex ?[31m?[36mGenerates a BAM index ".bai" file. ?[0m
?[32m CleanSam ?[31m?[36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads?[0m
?[32m CollectDuplicateMetrics ?[31m?[36mCollect Duplicate metrics from marked file.?[0m
?[32m DownsampleSam ?[31m?[36mDownsample a SAM or BAM file.?[0m
?[32m FastqToSam ?[31m?[36mConverts a FASTQ file to an unaligned BAM or SAM file?[0m
?[32m FilterSamReads ?[31m?[36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.?[0m
?[32m FixMateInformation ?[31m?[36mVerify mate-pair information between mates and fix if needed.?[0m
?[32m GatherBamFiles ?[31m?[36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis?[0m
?[32m MarkDuplicates ?[31m?[36mIdentifies duplicate reads. ?[0m
?[32m MarkDuplicatesWithMateCigar ?[31m?[36mIdentifies duplicate reads, accounting for mate CIGAR. ?[0m
?[32m MergeBamAlignment ?[31m?[36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. ?[0m
?[32m MergeSamFiles ?[31m?[36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. ?[0m
?[32m PositionBasedDownsampleSam ?[31m?[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 ReorderSam ?[31m?[36mReorders reads in a SAM or BAM file to match ordering in a second reference file.?[0m
?[32m ReplaceSamHeader ?[31m?[36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. ?[0m
?[32m RevertOriginalBaseQualitiesAndAddMateCigar ?[31m?[36mReverts the original base qualities and adds the mate cigar tag to read-group files?[0m
?[32m RevertSam ?[31m?[36mReverts SAM/BAM/CRAM files to a previous state. ?[0m
?[32m SamFormatConverter ?[31m?[36mConvert a BAM file to a SAM file, or a SAM to a BAM?[0m
?[32m SamToFastq ?[31m?[36mConverts a SAM/BAM/CRAM file to FASTQ.?[0m
?[32m SamToFastqWithTags ?[31m?[36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.?[0m
?[32m SetNmAndUqTags ?[31m?[36mDEPRECATED: Use SetNmMdAndUqTags instead.?[0m
?[32m SetNmMdAndUqTags ?[31m?[36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file ?[0m
?[32m SimpleMarkDuplicatesWithMateCigar ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.?[0m
?[32m SortSam ?[31m?[36mSorts a SAM, BAM or CRAM file. ?[0m
?[32m SplitSamByLibrary ?[31m?[36mSplits a SAM/BAM/CRAM file into individual files by library?[0m
?[32m SplitSamByNumberOfReads ?[31m?[36mSplits a SAM/BAM/CRAM file to multiple files.?[0m
?[32m UmiAwareMarkDuplicatesWithMateCigar ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mIdentifies duplicate reads using information from read positions and UMIs. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mReference: Tools that analyze and manipulate FASTA format references?[0m
?[32m BaitDesigner ?[31m?[36mDesigns oligonucleotide baits for hybrid selection reactions.?[0m
?[32m CreateSequenceDictionary ?[31m?[36mCreates a sequence dictionary for a reference sequence. ?[0m
?[32m ExtractSequences ?[31m?[36mSubsets intervals from a reference sequence to a new FASTA file.?[0m
?[32m NonNFastaSize ?[31m?[36mCounts the number of non-N bases in a fasta file.?[0m
?[32m NormalizeFasta ?[31m?[36mNormalizes lines of sequence in a FASTA file to be of the same length.?[0m
?[32m ScatterIntervalsByNs ?[31m?[36mWrites an interval list created by splitting a reference at Ns.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mTest Tools: Tools for internal test purposes ?[0m
?[32m MockCLP ?[31m?[36mNo-op CLP for testing initialization behavior.?[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 FindMendelianViolations ?[31m?[36mFinds mendelian violations of all types within a VCF?[0m
?[32m GenotypeConcordance ?[31m?[36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Filtering: Tools that filter variants by annotating the FILTER column?[0m
?[32m FilterVcf ?[31m?[36mHard filters a VCF.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data?[0m
?[32m FixVcfHeader ?[31m?[36mReplaces or fixes a VCF header.?[0m
?[32m GatherVcfs ?[31m?[36mGathers multiple VCF files from a scatter operation into a single VCF file?[0m
?[32m LiftoverVcf ?[31m?[36mLifts over a VCF file from one reference build to another. ?[0m
?[32m MakeSitesOnlyVcf ?[31m?[36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.?[0m
?[32m MakeVcfSampleNameMap ?[31m?[36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.?[0m
?[32m MergeVcfs ?[31m?[36mCombines multiple variant files into a single variant file?[0m
?[32m RenameSampleInVcf ?[31m?[36mRenames a sample within a VCF or BCF.?[0m
?[32m SortVcf ?[31m?[36mSorts one or more VCF files. ?[0m
?[32m SplitVcfs ?[31m?[36mSplits SNPs and INDELs into separate files. ?[0m
?[32m UpdateVcfSequenceDictionary ?[31m?[36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.?[0m
?[32m VcfFormatConverter ?[31m?[36mConverts VCF to BCF or BCF to VCF. ?[0m
?[32m VcfToIntervalList ?[31m?[36mConverts a VCF or BCF file to a Picard Interval List?[0m
?[37m--------------------------------------------------------------------------------------
?[0m'' is not a valid command. See PicardCommandLine -h for more information.
WARNING 2025-04-24 13:00:14 CommandLineSyntaxTranslater !!!!!!Possible mixed (legacy and new style) arguments detected!!!!!!!
Assuming new-style arguments are intended. See: https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
WARNING 2025-04-24 13:00:14 CommandLineSyntaxTranslater !!!!!!Possible mixed (legacy and new style) arguments detected!!!!!!!
Assuming new-style arguments are intended. See: https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
WARNING 2025-04-24 13:00:14 CommandLineSyntaxTranslater !!!!!!Possible mixed (legacy and new style) arguments detected!!!!!!!
Assuming new-style arguments are intended. See: https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
?[1m?[31mUSAGE: PicardCommandLine ?[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 ?[31m?[36mAsserts the validity for specified Illumina basecalling data. ?[0m
?[32m CollectIlluminaBasecallingMetrics ?[31m?[36mCollects Illumina Basecalling metrics for a sequencing run. ?[0m
?[32m CollectIlluminaLaneMetrics ?[31m?[36mCollects Illumina lane metrics for the given BaseCalling analysis directory.?[0m
?[32m ExtractIlluminaBarcodes ?[31m?[36mTool determines the barcode for each read in an Illumina lane. ?[0m
?[32m IlluminaBasecallsToFastq ?[31m?[36mGenerate FASTQ file(s) from Illumina basecall read data. ?[0m
?[32m IlluminaBasecallsToSam ?[31m?[36mTransforms raw Illumina sequencing data into an unmapped SAM, BAM or CRAM file.?[0m
?[32m MarkIlluminaAdapters ?[31m?[36mReads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mDiagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics?[0m
?[32m AccumulateQualityYieldMetrics ?[31m?[36mCombines multiple QualityYieldMetrics files into a single file.?[0m
?[32m AccumulateVariantCallingMetrics ?[31m?[36mCombines multiple Variant Calling Metrics files into a single file?[0m
?[32m BamIndexStats ?[31m?[36mGenerate index statistics from a BAM file?[0m
?[32m CalculateFingerprintMetrics ?[31m?[36mCalculate statistics on fingerprints, checking their viability?[0m
?[32m CalculateReadGroupChecksum ?[31m?[36mCreates a hash code based on the read groups (RG). ?[0m
?[32m CheckDuplicateMarking ?[31m?[36mChecks the consistency of duplicate markings.?[0m
?[32m CheckFingerprint ?[31m?[36mComputes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes?[0m
?[32m CheckTerminatorBlock ?[31m?[36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise?[0m
?[32m ClusterCrosscheckMetrics ?[31m?[36mClusters the results of a CrosscheckFingerprints run by LOD score?[0m
?[32m CollectAlignmentSummaryMetrics ?[31m?[36m<b>Produces a summary of alignment metrics from a SAM or BAM file.</b> ?[0m
?[32m CollectArraysVariantCallingMetrics ?[31m?[36mCollects summary and per-sample from the provided arrays VCF file?[0m
?[32m CollectBaseDistributionByCycle ?[31m?[36mChart the nucleotide distribution per cycle in a SAM or BAM file?[0m
?[32m CollectGcBiasMetrics ?[31m?[36mCollect metrics regarding GC bias. ?[0m
?[32m CollectHiSeqXPfFailMetrics ?[31m?[36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.?[0m
?[32m CollectHsMetrics ?[31m?[36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. ?[0m
?[32m CollectIndependentReplicateMetrics ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mEstimates the rate of independent replication rate of reads within a bam.
?[0m
?[32m CollectInsertSizeMetrics ?[31m?[36mCollect metrics about the insert size distribution of a paired-end library. ?[0m
?[32m CollectJumpingLibraryMetrics ?[31m?[36mCollect jumping library metrics. ?[0m
?[32m CollectMultipleMetrics ?[31m?[36mCollect multiple classes of metrics. ?[0m
?[32m CollectOxoGMetrics ?[31m?[36mCollect metrics to assess oxidative artifacts.?[0m
?[32m CollectQualityYieldMetrics ?[31m?[36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. ?[0m
?[32m CollectQualityYieldMetricsFlow ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mCollect metrics about reads that pass quality thresholds from flow based read files. ?[0m
?[32m CollectQualityYieldMetricsSNVQ ?[31m?[36mCollect SNVQ metrics about reads that pass quality thresholds and other filters (such as vendor fail, etc). ?[0m
?[32m CollectRawWgsMetrics ?[31m?[36mCollect whole genome sequencing-related metrics. ?[0m
?[32m CollectRnaSeqMetrics ?[31m?[36mProduces RNA alignment metrics for a SAM or BAM file. ?[0m
?[32m CollectRrbsMetrics ?[31m?[36m<b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b> ?[0m
?[32m CollectSamErrorMetrics ?[31m?[36mProgram to collect error metrics on bases stratified in various ways.?[0m
?[32m CollectSequencingArtifactMetrics ?[31m?[36mCollect metrics to quantify single-base sequencing artifacts. ?[0m
?[32m CollectTargetedPcrMetrics ?[31m?[36mCalculate PCR-related metrics from targeted sequencing data. ?[0m
?[32m CollectUmiPrevalenceMetrics ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mTally the counts of UMIs in duplicate sets within a bam.
?[0m
?[32m CollectVariantCallingMetrics ?[31m?[36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file?[0m
?[32m CollectWgsMetrics ?[31m?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.?[0m
?[32m CollectWgsMetricsWithNonZeroCoverage ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. ?[0m
?[32m CompareMetrics ?[31m?[36mCompare two metrics files.?[0m
?[32m CompareSAMs ?[31m?[36mCompare two input SAM/BAM/CRAM files. ?[0m
?[32m ConvertHaplotypeDatabaseToVcf ?[31m?[36mConvert Haplotype database file to vcf?[0m
?[32m ConvertSequencingArtifactToOxoG ?[31m?[36mExtract OxoG metrics from generalized artifacts metrics. ?[0m
?[32m CrosscheckFingerprints ?[31m?[36mChecks that all data in the input files appear to have come from the same individual?[0m
?[32m CrosscheckReadGroupFingerprints ?[31m?[36mDEPRECATED: USE CrosscheckFingerprints. ?[0m
?[32m EstimateLibraryComplexity ?[31m?[36mEstimates the numbers of unique molecules in a sequencing library. ?[0m
?[32m ExtractFingerprint ?[31m?[36mComputes a fingerprint from the input file.?[0m
?[32m IdentifyContaminant ?[31m?[36mComputes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.?[0m
?[32m LiftOverHaplotypeMap ?[31m?[36mLifts over a haplotype database from one reference to another?[0m
?[32m MeanQualityByCycle ?[31m?[36mCollect mean quality by cycle.?[0m
?[32m QualityScoreDistribution ?[31m?[36mChart the distribution of quality scores. ?[0m
?[32m ValidateSamFile ?[31m?[36mValidates a SAM/BAM/CRAM file.?[0m
?[32m ViewSam ?[31m?[36mPrints a SAM or BAM file to the screen?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mGenotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays?[0m
?[32m BpmToNormalizationManifestCsv ?[31m?[36mProgram to convert an Illumina bpm file into a bpm.csv file.?[0m
?[32m CombineGenotypingArrayVcfs ?[31m?[36mProgram to combine multiple genotyping array VCF files into one VCF.?[0m
?[32m CompareGtcFiles ?[31m?[36mCompares two GTC files.?[0m
?[32m CreateBafRegressMetricsFile ?[31m?[36mProgram to generate a picard metrics file from the output of the bafRegress tool.?[0m
?[32m CreateExtendedIlluminaManifest ?[31m?[36mCreate an Extended Illumina Manifest for usage by the Picard tool GtcToVcf?[0m
?[32m CreateVerifyIDIntensityContaminationMetricsFile ?[31m?[36mProgram to generate a picard metrics file from the output of the VerifyIDIntensity tool.?[0m
?[32m GtcToVcf ?[31m?[36mProgram to convert an Illumina GTC file to a VCF?[0m
?[32m MergePedIntoVcf ?[31m?[36mProgram to merge a single-sample ped file from zCall into a single-sample VCF.?[0m
?[32m VcfToAdpc ?[31m?[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 ?[31m?[36mConverts a BED file to a Picard Interval List. ?[0m
?[32m IntervalListToBed ?[31m?[36mConverts an Picard IntervalList file to a BED file.?[0m
?[32m IntervalListTools ?[31m?[36mA tool for performing various IntervalList manipulations?[0m
?[32m LiftOverIntervalList ?[31m?[36mLifts over an interval list from one reference build to another. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mOther: Miscellaneous tools, e.g. those that aid in data streaming?[0m
?[32m FifoBuffer ?[31m?[36mProvides a large, FIFO buffer that can be used to buffer input and output streams between programs.?[0m
?[32m SortGff ?[31m?[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 ?[31m?[36mAdds comments to the header of a BAM file.?[0m
?[32m AddOATag ?[31m?[36mRecord current alignment information to OA tag.?[0m
?[32m AddOrReplaceReadGroups ?[31m?[36mAssigns all the reads in a file to a single new read-group.?[0m
?[32m BamToBfq ?[31m?[36mConverts a BAM file into a BFQ (binary fastq formatted) file?[0m
?[32m BuildBamIndex ?[31m?[36mGenerates a BAM index ".bai" file. ?[0m
?[32m CleanSam ?[31m?[36mCleans a SAM/BAM/CRAM files, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads?[0m
?[32m CollectDuplicateMetrics ?[31m?[36mCollect Duplicate metrics from marked file.?[0m
?[32m DownsampleSam ?[31m?[36mDownsample a SAM or BAM file.?[0m
?[32m FastqToSam ?[31m?[36mConverts a FASTQ file to an unaligned BAM or SAM file?[0m
?[32m FilterSamReads ?[31m?[36mSubsets reads from a SAM/BAM/CRAM file by applying one of several filters.?[0m
?[32m FixMateInformation ?[31m?[36mVerify mate-pair information between mates and fix if needed.?[0m
?[32m GatherBamFiles ?[31m?[36mConcatenate efficiently BAM files that resulted from a scattered parallel analysis?[0m
?[32m MarkDuplicates ?[31m?[36mIdentifies duplicate reads. ?[0m
?[32m MarkDuplicatesWithMateCigar ?[31m?[36mIdentifies duplicate reads, accounting for mate CIGAR. ?[0m
?[32m MergeBamAlignment ?[31m?[36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. ?[0m
?[32m MergeSamFiles ?[31m?[36mMerges multiple SAM/BAM/CRAM (and/or) files into a single file. ?[0m
?[32m PositionBasedDownsampleSam ?[31m?[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 ReorderSam ?[31m?[36mReorders reads in a SAM or BAM file to match ordering in a second reference file.?[0m
?[32m ReplaceSamHeader ?[31m?[36mReplaces the SAMFileHeader in a SAM/BAM/CRAM file. ?[0m
?[32m RevertOriginalBaseQualitiesAndAddMateCigar ?[31m?[36mReverts the original base qualities and adds the mate cigar tag to read-group files?[0m
?[32m RevertSam ?[31m?[36mReverts SAM/BAM/CRAM files to a previous state. ?[0m
?[32m SamFormatConverter ?[31m?[36mConvert a BAM file to a SAM file, or a SAM to a BAM?[0m
?[32m SamToFastq ?[31m?[36mConverts a SAM/BAM/CRAM file to FASTQ.?[0m
?[32m SamToFastqWithTags ?[31m?[36mConverts a SAM or BAM file to FASTQ alongside FASTQs created from tags.?[0m
?[32m SetNmAndUqTags ?[31m?[36mDEPRECATED: Use SetNmMdAndUqTags instead.?[0m
?[32m SetNmMdAndUqTags ?[31m?[36mFixes the NM, MD, and UQ tags in a SAM/BAM/CRAM file ?[0m
?[32m SimpleMarkDuplicatesWithMateCigar ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.?[0m
?[32m SortSam ?[31m?[36mSorts a SAM, BAM or CRAM file. ?[0m
?[32m SplitSamByLibrary ?[31m?[36mSplits a SAM/BAM/CRAM file into individual files by library?[0m
?[32m SplitSamByNumberOfReads ?[31m?[36mSplits a SAM/BAM/CRAM file to multiple files.?[0m
?[32m UmiAwareMarkDuplicatesWithMateCigar ?[31m**EXPERIMENTAL - USE AT YOUR OWN RISK** ?[36mIdentifies duplicate reads using information from read positions and UMIs. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mReference: Tools that analyze and manipulate FASTA format references?[0m
?[32m BaitDesigner ?[31m?[36mDesigns oligonucleotide baits for hybrid selection reactions.?[0m
?[32m CreateSequenceDictionary ?[31m?[36mCreates a sequence dictionary for a reference sequence. ?[0m
?[32m ExtractSequences ?[31m?[36mSubsets intervals from a reference sequence to a new FASTA file.?[0m
?[32m NonNFastaSize ?[31m?[36mCounts the number of non-N bases in a fasta file.?[0m
?[32m NormalizeFasta ?[31m?[36mNormalizes lines of sequence in a FASTA file to be of the same length.?[0m
?[32m ScatterIntervalsByNs ?[31m?[36mWrites an interval list created by splitting a reference at Ns.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mTest Tools: Tools for internal test purposes ?[0m
?[32m MockCLP ?[31m?[36mNo-op CLP for testing initialization behavior.?[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 FindMendelianViolations ?[31m?[36mFinds mendelian violations of all types within a VCF?[0m
?[32m GenotypeConcordance ?[31m?[36mCalculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Filtering: Tools that filter variants by annotating the FILTER column?[0m
?[32m FilterVcf ?[31m?[36mHard filters a VCF.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVariant Manipulation: Tools that manipulate variant call format (VCF) data?[0m
?[32m FixVcfHeader ?[31m?[36mReplaces or fixes a VCF header.?[0m
?[32m GatherVcfs ?[31m?[36mGathers multiple VCF files from a scatter operation into a single VCF file?[0m
?[32m LiftoverVcf ?[31m?[36mLifts over a VCF file from one reference build to another. ?[0m
?[32m MakeSitesOnlyVcf ?[31m?[36mCreates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.?[0m
?[32m MakeVcfSampleNameMap ?[31m?[36mCreates a TSV from sample name to VCF/GVCF path, with one line per input.?[0m
?[32m MergeVcfs ?[31m?[36mCombines multiple variant files into a single variant file?[0m
?[32m RenameSampleInVcf ?[31m?[36mRenames a sample within a VCF or BCF.?[0m
?[32m SortVcf ?[31m?[36mSorts one or more VCF files. ?[0m
?[32m SplitVcfs ?[31m?[36mSplits SNPs and INDELs into separate files. ?[0m
?[32m UpdateVcfSequenceDictionary ?[31m?[36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.?[0m
?[32m VcfFormatConverter ?[31m?[36mConverts VCF to BCF or BCF to VCF. ?[0m
?[32m VcfToIntervalList ?[31m?[36mConverts a VCF or BCF file to a Picard Interval List?[0m
?[37m--------------------------------------------------------------------------------------
?[0m