?[1m?[31mUSAGE: PicardCommandLine ?[32m<program name>?[1m?[31m [-h]
?[0m?[1m?[31mAvailable Programs:
?[0m?[37m--------------------------------------------------------------------------------------
?[0m?[31mAlpha Tools: Tools that are currently UNSUPPORTED until further testing and maturation.?[0m
?[32m CheckFingerprint ?[36mComputes a fingerprint from the supplied SAM/BAM file and compares it to the provided genotypes?[0m
?[32m CollectIndependentReplicateMetrics ?[36mEstimates the rate of independent replication of reads within a bam.?[0m
?[32m CollectWgsMetricsWithNonZeroCoverage ?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments. ?[0m
?[32m CrosscheckReadGroupFingerprints ?[36mChecks if all read groups appear to come from the same individual?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mFasta: Tools for manipulating FASTA, or related data.?[0m
?[32m CreateSequenceDictionary ?[36mCreates a sequence dictionary for a reference sequence. ?[0m
?[32m ExtractSequences ?[36mSubsets intervals from a reference sequence to a new FASTA file.?[0m
?[32m NonNFastaSize ?[36mCounts the number of non-N bases in a fasta file.?[0m
?[32m NormalizeFasta ?[36mNormalizes lines of sequence in a FASTA file to be of the same length.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mIllumina Tools: Tools for manipulating data specific to Illumina sequencers.?[0m
?[32m CheckIlluminaDirectory ?[36mAsserts the validity for specified Illumina basecalling data. ?[0m
?[32m CollectIlluminaBasecallingMetrics ?[36mCollects Illumina Basecalling metrics for a sequencing run. ?[0m
?[32m CollectIlluminaLaneMetrics ?[36mCollects Illumina lane metrics for the given BaseCalling analysis directory. ?[0m
?[32m ExtractIlluminaBarcodes ?[36mTool determines the barcode for each read in an Illumina lane. ?[0m
?[32m IlluminaBasecallsToFastq ?[36mGenerate FASTQ file(s) from Illumina basecall read data. ?[0m
?[32m IlluminaBasecallsToSam ?[36mTransforms raw Illumina sequencing data into an unmapped SAM or BAM file.?[0m
?[32m MarkIlluminaAdapters ?[36mReads a SAM or BAM file and rewrites it with new adapter-trimming tags. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mInterval Tools: Tools for manipulating Picard interval lists.?[0m
?[32m BedToIntervalList ?[36mConverts a BED file to a Picard Interval List. ?[0m
?[32m IntervalListToBed ?[36mConverts an Picard IntervalList file to a BED file.?[0m
?[32m IntervalListTools ?[36mManipulates interval lists. ?[0m
?[32m LiftOverIntervalList ?[36mLifts over an interval list from one reference build to another. ?[0m
?[32m ScatterIntervalsByNs ?[36mWrites an interval list based on splitting a reference by Ns. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mMetrics: Tools for reporting metrics on various data types.?[0m
?[32m CalculateHsMetrics ?[36mDEPRECATED: Use CollectHsMetrics instead.?[0m
?[32m CollectAlignmentSummaryMetrics ?[36m<b>Produces a summary of alignment metrics from a SAM or BAM file.</b> ?[0m
?[32m CollectBaseDistributionByCycle ?[36mChart the nucleotide distribution per cycle in a SAM or BAM file?[0m
?[32m CollectGcBiasMetrics ?[36mCollect metrics regarding GC bias. ?[0m
?[32m CollectHiSeqXPfFailMetrics ?[36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.?[0m
?[32m CollectHsMetrics ?[36mCollects hybrid-selection (HS) metrics for a SAM or BAM file. ?[0m
?[32m CollectInsertSizeMetrics ?[36mCollect metrics about the insert size distribution of a paired-end library.?[0m
?[32m CollectJumpingLibraryMetrics ?[36mCollect jumping library metrics. ?[0m
?[32m CollectMultipleMetrics ?[36mCollect multiple classes of metrics. ?[0m
?[32m CollectOxoGMetrics ?[36mCollect metrics to assess oxidative artifacts.?[0m
?[32m CollectQualityYieldMetrics ?[36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters. ?[0m
?[32m CollectRawWgsMetrics ?[36mCollect whole genome sequencing-related metrics. ?[0m
?[32m CollectRnaSeqMetrics ?[36mProduces RNA alignment metrics for a SAM or BAM file. ?[0m
?[32m CollectRrbsMetrics ?[36m<b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b> ?[0m
?[32m CollectSequencingArtifactMetrics ?[36mCollect metrics to quantify single-base sequencing artifacts. ?[0m
?[32m CollectTargetedPcrMetrics ?[36mCalculate PCR-related metrics from targeted sequencing data. ?[0m
?[32m CollectVariantCallingMetrics ?[36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file?[0m
?[32m CollectWgsMetrics ?[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.?[0m
?[32m CollectWgsMetricsFromQuerySorted ?[36mWrites sequencing-related metrics for a SAM or BAM file?[0m
?[32m CollectWgsMetricsFromSampledSites ?[36mWrites whole genome sequencing-related metrics for a SAM or BAM file?[0m
?[32m CompareMetrics ?[36mCompare two metrics files.?[0m
?[32m ConvertSequencingArtifactToOxoG ?[36mExtract OxoG metrics from generalized artifacts metrics. ?[0m
?[32m EstimateLibraryComplexity ?[36mEstimates the numbers of unique molecules in a sequencing library. ?[0m
?[32m MeanQualityByCycle ?[36mCollect mean quality by cycle.?[0m
?[32m QualityScoreDistribution ?[36mChart the distribution of quality scores. ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mMiscellaneous Tools: A set of miscellaneous tools. ?[0m
?[32m BaitDesigner ?[36m<b>Designs oligonucleotide baits for hybrid selection reactions.</b> ?[0m
?[32m FifoBuffer ?[36mFIFO buffer used to buffer input and output streams with a customizable buffer size ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mSAM/BAM: Tools for manipulating SAM, BAM, or related data.?[0m
?[32m AddCommentsToBam ?[36mAdds comments to the header of a BAM file.?[0m
?[32m AddOrReplaceReadGroups ?[36mReplace read groups in a BAM file.?[0m
?[32m BamIndexStats ?[36mGenerate index statistics from a BAM file?[0m
?[32m BamToBfq ?[36mCreate BFQ files from a BAM file for use by the maq aligner. ?[0m
?[32m BuildBamIndex ?[36mGenerates a BAM index ".bai" file. ?[0m
?[32m CalculateReadGroupChecksum ?[36mCreates a hash code based on the read groups (RG). ?[0m
?[32m CheckTerminatorBlock ?[36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise?[0m
?[32m CleanSam ?[36mCleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads?[0m
?[32m CompareSAMs ?[36mCompare two input ".sam" or ".bam" files. ?[0m
?[32m DownsampleSam ?[36mDownsample a SAM or BAM file. ?[0m
?[32m FastqToSam ?[36mConverts a FASTQ file to an unaligned BAM or SAM file. ?[0m
?[32m FilterSamReads ?[36mSubset read data from a SAM or BAM file?[0m
?[32m FixMateInformation ?[36mVerify mate-pair information between mates and fix if needed.?[0m
?[32m GatherBamFiles ?[36mConcatenate one or more BAM files as efficiently as possible?[0m
?[32m MarkDuplicates ?[36mIdentifies duplicate reads. ?[0m
?[32m MarkDuplicatesWithMateCigar ?[36mIdentifies duplicate reads, accounting for mate CIGAR. ?[0m
?[32m MergeBamAlignment ?[36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file. ?[0m
?[32m MergeSamFiles ?[36mMerges multiple SAM and/or BAM files into a single file. ?[0m
?[32m PositionBasedDownsampleSam ?[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 ?[36mReorders reads in a SAM or BAM file to match ordering in reference?[0m
?[32m ReplaceSamHeader ?[36mReplaces the SAMFileHeader in a SAM or BAM file. ?[0m
?[32m RevertOriginalBaseQualitiesAndAddMateCigar ?[36mReverts the original base qualities and adds the mate cigar tag to read-group BAMs?[0m
?[32m RevertSam ?[36mReverts SAM or BAM files to a previous state. ?[0m
?[32m SamFormatConverter ?[36mConvert a BAM file to a SAM file, or a SAM to a BAM?[0m
?[32m SamToFastq ?[36mConverts a SAM or BAM file to FASTQ. ?[0m
?[32m SetNmAndUqTags ?[36mFixes the UQ and NM tags in a SAM file. ?[0m
?[32m SortSam ?[36mSorts a SAM or BAM file. ?[0m
?[32m SplitSamByLibrary ?[36mSplits a SAM or BAM file into individual files by library?[0m
?[32m ValidateSamFile ?[36mValidates a SAM or BAM file. ?[0m
?[32m ViewSam ?[36mPrints a SAM or BAM file to the screen?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mUnit Testing: Unit testing ?[0m
?[32m SimpleMarkDuplicatesWithMateCigar ?[36mExamines aligned records in the supplied SAM or BAM file to locate duplicate molecules.?[0m
?[32m TestParserFail ?[36mThis tool offers.....?[0m
?[32m TestParserSucceed ?[36m X < Y ?[0m
?[37m--------------------------------------------------------------------------------------
?[0m?[31mVCF/BCF: Tools for manipulating VCF, BCF, or related data.?[0m
?[32m FilterVcf ?[36mHard filters a VCF.?[0m
?[32m FixVcfHeader ?[36mReplaces or fixes a VCF header.?[0m
?[32m GatherVcfs ?[36mGathers multiple VCF files from a scatter operation into a single VCF file?[0m
?[32m GenotypeConcordance ?[36mEvaluate genotype concordance between callsets.?[0m
?[32m LiftoverVcf ?[36mLifts over a VCF file from one reference build to another. ?[0m
?[32m MakeSitesOnlyVcf ?[36mCreates a VCF bereft of genotype information from an input VCF or BCF?[0m
?[32m MergeVcfs ?[36mMerges multiple VCF or BCF files into one VCF file or BCF?[0m
?[32m RenameSampleInVcf ?[36mRenames a sample within a VCF or BCF. ?[0m
?[32m SortVcf ?[36mSorts one or more VCF files. ?[0m
?[32m SplitVcfs ?[36mSplits SNPs and INDELs into separate files. ?[0m
?[32m UpdateVcfSequenceDictionary ?[36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.?[0m
?[32m VcfFormatConverter ?[36mConverts VCF to BCF or BCF to VCF. ?[0m
?[32m VcfToIntervalList ?[36mConverts a VCF or BCF file to a Picard Interval List.?[0m
?[37m--------------------------------------------------------------------------------------
?[0m'' is not a valid command. See PicardCommandLine --help for more information.