Picard tools

USAGE: PicardCommandLine <program name> [-h]

Available Programs:
Base Calling:                                    Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters
    CheckIlluminaDirectory                       Asserts the validity for specified Illumina basecalling data.  
    CollectIlluminaBasecallingMetrics            Collects Illumina Basecalling metrics for a sequencing run.  
    CollectIlluminaLaneMetrics                   Collects Illumina lane metrics for the given BaseCalling analysis directory.  
    ExtractIlluminaBarcodes                      Tool determines the barcode for each read in an Illumina lane.  
    IlluminaBasecallsToFastq                     Generate FASTQ file(s) from Illumina basecall read data.  
    IlluminaBasecallsToSam                       Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.
    MarkIlluminaAdapters                         Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.  

Diagnostics and Quality Control:                 Tools that collect sequencing quality related and comparative metrics
    AccumulateVariantCallingMetrics              Combines multiple Variant Calling Metrics files into a single file
    BamIndexStats                                Generate index statistics from a BAM file
    CalculateReadGroupChecksum                   Creates a hash code based on the read groups (RG).  
    CheckFingerprint                             Computes a fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the provided genotypes
    CheckTerminatorBlock                         Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise
    ClusterCrosscheckMetrics                     Clusters the results of a CrosscheckFingerprints run by LOD score
    CollectAlignmentSummaryMetrics               <b>Produces a summary of alignment metrics from a SAM or BAM file.</b>  
    CollectBaseDistributionByCycle               Chart the nucleotide distribution per cycle in a SAM or BAM file
    CollectGcBiasMetrics                         Collect metrics regarding GC bias. 
    CollectHiSeqXPfFailMetrics                   Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
    CollectHsMetrics                             Collects hybrid-selection (HS) metrics for a SAM or BAM file.  
    CollectIndependentReplicateMetrics           **EXPERIMENTAL FEATURE - USE AT YOUR OWN RISK** Estimates the rate of independent replication of reads within a bam.
    CollectInsertSizeMetrics                     Collect metrics about the insert size distribution of a paired-end library.
    CollectJumpingLibraryMetrics                 Collect jumping library metrics. 
    CollectMultipleMetrics                       Collect multiple classes of metrics.  
    CollectOxoGMetrics                           Collect metrics to assess oxidative artifacts.
    CollectQualityYieldMetrics                   Collect metrics about reads that pass quality thresholds and Illumina-specific filters.  
    CollectRawWgsMetrics                         Collect whole genome sequencing-related metrics.  
    CollectRnaSeqMetrics                         Produces RNA alignment metrics for a SAM or BAM file.  
    CollectRrbsMetrics                           <b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b>  
    CollectSequencingArtifactMetrics             Collect metrics to quantify single-base sequencing artifacts.  
    CollectTargetedPcrMetrics                    Calculate PCR-related metrics from targeted sequencing data. 
    CollectVariantCallingMetrics                 Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file
    CollectWgsMetrics                            Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
    CollectWgsMetricsWithNonZeroCoverage         **EXPERIMENTAL FEATURE - USE AT YOUR OWN RISK** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  
    CompareMetrics                               Compare two metrics files.
    CompareSAMs                                  Compare two input ".sam" or ".bam" files.  
    ConvertSequencingArtifactToOxoG              Extract OxoG metrics from generalized artifacts metrics.  
    CrosscheckFingerprints                       Checks that all data in the input files appear to have come from the same individual
    CrosscheckReadGroupFingerprints              DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups appear to come from the same individual.
    EstimateLibraryComplexity                    Estimates the numbers of unique molecules in a sequencing library.  
    IdentifyContaminant                          Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.
    MeanQualityByCycle                           Collect mean quality by cycle.
    QualityScoreDistribution                     Chart the distribution of quality scores.  
    ValidateSamFile                              Validates a SAM or BAM file.
    ViewSam                                      Prints a SAM or BAM file to the screen

Intervals Manipulation:                          Tools that process genomic intervals in various formats
    BedToIntervalList                            Converts a BED file to a Picard Interval List.  
    IntervalListToBed                            Converts an Picard IntervalList file to a BED file.
    IntervalListTools                            A tool for performing various IntervalList manipulations
    LiftOverIntervalList                         Lifts over an interval list from one reference build to another. 

Other:                                           Miscellaneous tools, e.g. those that aid in data streaming
    FifoBuffer                                   Provides a large, FIFO buffer that can be used to buffer input and output streams between programs.

Read Data Manipulation:                          Tools that manipulate read data in SAM, BAM or CRAM format
    AddCommentsToBam                             Adds comments to the header of a BAM file.
    AddOrReplaceReadGroups                       Assigns all the reads in a file to a single new read-group.
    BamToBfq                                     Converts a BAM file into a BFQ (binary fastq formatted) file
    BuildBamIndex                                Generates a BAM index ".bai" file.  
    CleanSam                                     Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
    DownsampleSam                                Downsample a SAM or BAM file.
    FastqToSam                                   Converts a FASTQ file to an unaligned BAM or SAM file
    FilterSamReads                               Subsets reads from a SAM or BAM file by applying one of several filters.
    FixMateInformation                           Verify mate-pair information between mates and fix if needed.
    GatherBamFiles                               Concatenate efficiently BAM files that resulted from a scattered parallel analysis
    MarkDuplicates                               Identifies duplicate reads.  
    MarkDuplicatesWithMateCigar                  Identifies duplicate reads, accounting for mate CIGAR.  
    MergeBamAlignment                            Merge alignment data from a SAM or BAM with data in an unmapped BAM file.  
    MergeSamFiles                                Merges multiple SAM and/or BAM files into a single file.  
    PositionBasedDownsampleSam                   Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.
    ReorderSam                                   Reorders reads in a SAM or BAM file to match ordering in a second reference file.
    ReplaceSamHeader                             Replaces the SAMFileHeader in a SAM or BAM file.  
    RevertOriginalBaseQualitiesAndAddMateCigar   Reverts the original base qualities and adds the mate cigar tag to read-group BAMs
    RevertSam                                    Reverts SAM or BAM files to a previous state.  
    SamFormatConverter                           Convert a BAM file to a SAM file, or a SAM to a BAM
    SamToFastq                                   Converts a SAM or BAM file to FASTQ.
    SamToFastqWithTags                           Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags.
    SetNmAndUqTags                               DEPRECATED: Use SetNmMdAndUqTags instead.
    SetNmMdAndUqTags                             Fixes the NM, MD, and UQ tags in a SAM file 
    SimpleMarkDuplicatesWithMateCigar            **EXPERIMENTAL FEATURE - USE AT YOUR OWN RISK** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
    SortSam                                      Sorts a SAM or BAM file
    SplitSamByLibrary                            Splits a SAM or BAM file into individual files by library
    SplitSamByNumberOfReads                      Splits a SAM or BAM file to multiple BAMs.
    UmiAwareMarkDuplicatesWithMateCigar          **EXPERIMENTAL FEATURE - USE AT YOUR OWN RISK** Identifies duplicate reads using information from read positions and UMIs. 

Reference:                                       Tools that analyze and manipulate FASTA format references
    BaitDesigner                                 Designs oligonucleotide baits for hybrid selection reactions.
    CreateSequenceDictionary                     Creates a sequence dictionary for a reference sequence.  
    ExtractSequences                             Subsets intervals from a reference sequence to a new FASTA file.
    NonNFastaSize                                Counts the number of non-N bases in a fasta file.
    NormalizeFasta                               Normalizes lines of sequence in a FASTA file to be of the same length.
    ScatterIntervalsByNs                         Writes an interval list created by splitting a reference at Ns.

Variant Evaluation and Refinement:               Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine
    FindMendelianViolations                      Finds mendelian violations of all types within a VCF
    GenotypeConcordance                          Calculates the concordance between genotype data of one samples in each of two VCFs - one  being considered the truth (or reference) the other being the call.  The concordance is broken into separate results sections for SNPs and indels.  Statistics are reported in three different files.

Variant Filtering:                               Tools that filter variants by annotating the FILTER column
    FilterVcf                                    Hard filters a VCF.

Variant Manipulation:                            Tools that manipulate variant call format (VCF) data
    FixVcfHeader                                 Replaces or fixes a VCF header.
    GatherVcfs                                   Gathers multiple VCF files from a scatter operation into a single VCF file
    LiftoverVcf                                  Lifts over a VCF file from one reference build to another.  
    MakeSitesOnlyVcf                             Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
    MakeVcfSampleNameMap                         Creates a TSV from sample name to VCF/GVCF path, with one line per input.
    MergeVcfs                                    Combines multiple variant files into a single variant file
    RenameSampleInVcf                            Renames a sample within a VCF or BCF.
    SortVcf                                      Sorts one or more VCF files.  
    SplitVcfs                                    Splits SNPs and INDELs into separate files.  
    UpdateVcfSequenceDictionary                  Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.
    VcfFormatConverter                           Converts VCF to BCF or BCF to VCF.  
    VcfToIntervalList                            Converts a VCF or BCF file to a Picard Interval List