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USAGE: PicardCommandLine <program name> [-h]
Available Programs:
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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.
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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
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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.
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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.
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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.
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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.
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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.
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Variant Filtering: Tools that filter variants by annotating the FILTER column
FilterVcf Hard filters a VCF.
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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
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