Uses of Class
picard.cmdline.CommandLineProgram

Packages that use CommandLineProgram

Package	Description
picard.analysis
picard.analysis.artifacts
picard.analysis.directed
picard.analysis.replicates
picard.fastq
picard.fingerprint
picard.illumina
picard.illumina.quality
picard.reference
picard.sam
picard.sam.markduplicates
picard.sam.markduplicates.util
picard.util
picard.vcf
picard.vcf.filter

Uses of CommandLineProgram in picard.analysis

Subclasses of CommandLineProgram in picard.analysis

Modifier and Type	Class and Description
class	CollectAlignmentSummaryMetrics A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
class	CollectBaseDistributionByCycle
class	CollectGcBiasMetrics Tool to collect information about GC bias in the reads in a given BAM file.
class	CollectInsertSizeMetrics Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
class	CollectJumpingLibraryMetrics Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
class	CollectMultipleMetrics Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
class	CollectOxoGMetrics Class for trying to quantify the CpCG->CpCA error rate.
class	CollectQualityYieldMetrics Command line program to calibrate quality yield metrics
class	CollectRawWgsMetrics Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as CollectWgsMetrics, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap.
class	CollectRnaSeqMetrics
class	CollectRrbsMetrics Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
class	CollectWgsMetrics Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
class	CollectWgsMetricsFromQuerySorted Deprecated.
class	CollectWgsMetricsFromSampledSites Deprecated.
class	CollectWgsMetricsWithNonZeroCoverage
class	CompareMetrics Compare two metrics files.
class	MeanQualityByCycle Program to generate a data table and chart of mean quality by cycle from a BAM file.
class	QualityScoreDistribution Charts quality score distribution within a BAM file.
class	SinglePassSamProgram Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.

Uses of CommandLineProgram in picard.analysis.artifacts

Subclasses of CommandLineProgram in picard.analysis.artifacts

Modifier and Type	Class and Description
class	CollectSequencingArtifactMetrics Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
class	ConvertSequencingArtifactToOxoG

Uses of CommandLineProgram in picard.analysis.directed

Subclasses of CommandLineProgram in picard.analysis.directed

Modifier and Type	Class and Description
class	CalculateHsMetrics Deprecated.
class	CollectHsMetrics Collects a set of HS metrics from a sam or bam file.
class	CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>> Both CollectTargetedPCRMetrics and CalculateHybridSelection metrics share virtually identical program structures except for the name of their targeting mechanisms (e.g.
class	CollectTargetedPcrMetrics Collect metric information for target pcr metrics runs.

Uses of CommandLineProgram in picard.analysis.replicates

Subclasses of CommandLineProgram in picard.analysis.replicates

Modifier and Type	Class and Description
class	CollectIndependentReplicateMetrics A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.

Uses of CommandLineProgram in picard.fastq

Subclasses of CommandLineProgram in picard.fastq

Modifier and Type	Class and Description
class	BamToBfq CommandLineProgram to generate to bfq files for use by the Maq aligner

Uses of CommandLineProgram in picard.fingerprint

Subclasses of CommandLineProgram in picard.fingerprint

Modifier and Type	Class and Description
class	CheckFingerprint Attempts to check the sample identity of the sequence data in the provided SAM/BAM file against a set of known genotypes in the supplied genotype file (in either GELI or VCF format).
class	CrosscheckReadGroupFingerprints Program to check that all read groups within the set of BAM files appear to come from the same individual.

Uses of CommandLineProgram in picard.illumina

Subclasses of CommandLineProgram in picard.illumina

Modifier and Type	Class and Description
class	CheckIlluminaDirectory Program to check a lane of an Illumina output directory.
class	CollectIlluminaBasecallingMetrics A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
class	CollectIlluminaLaneMetrics Command-line wrapper around CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.
class	ExtractIlluminaBarcodes Determine the barcode for each read in an Illumina lane.
class	IlluminaBasecallsToFastq
class	IlluminaBasecallsToSam IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM or BAM file format.
class	MarkIlluminaAdapters Command line program to mark the location of adapter sequences.

Uses of CommandLineProgram in picard.illumina.quality

Subclasses of CommandLineProgram in picard.illumina.quality

Modifier and Type	Class and Description
class	CollectHiSeqXPfFailMetrics Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.

Uses of CommandLineProgram in picard.reference

Subclasses of CommandLineProgram in picard.reference

Modifier and Type	Class and Description
class	ExtractSequences Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
class	NonNFastaSize A tool to count the number of non-N bases in a fasta file
class	NormalizeFasta Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!

Uses of CommandLineProgram in picard.sam

Subclasses of CommandLineProgram in picard.sam

Modifier and Type	Class and Description
class	AddCommentsToBam A tool to add comments to a BAM file header.
class	AddOrReplaceReadGroups Replaces read groups in a BAM file
class	BamIndexStats Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
class	BuildBamIndex Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
class	CalculateReadGroupChecksum
class	CheckTerminatorBlock Simple class to check the terminator block of a SAM file.
class	CleanSam
class	CompareSAMs Rudimentary SAM comparer.
class	CreateSequenceDictionary Create a SAM/BAM file from a fasta containing reference sequence.
class	DownsampleSam Class to randomly downsample a BAM file while respecting that we should either retain or discard all of the reads for a template - i.e.
class	FastqToSam Converts a fastq file to an unaligned BAM/SAM format.
class	FilterSamReads From a SAM or BAM file, produce a new SAM or BAM by filtering aligned reads or a list of read names provided in a file (one readname per line) $Id$
class	FixMateInformation Class to fix mate pair information for all reads in a SAM file.
class	GatherBamFiles Program to perform a rapid "gather" operation on BAM files after a scatter operations where the same process has been performed on different regions of a BAM file creating many smaller BAM files that now need to be concatenated back together.
class	MergeBamAlignment A command-line tool to merge BAM/SAM alignment info from a third-party aligner with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM
class	MergeSamFiles Reads a SAM or BAM file and combines the output to one file
class	PositionBasedDownsampleSam Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither end of the pair.
class	ReorderSam Reorders a SAM/BAM input file according to the order of contigs in a second reference sequence
class	ReplaceSamHeader
class	RevertOriginalBaseQualitiesAndAddMateCigar This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped BAMs.
class	RevertSam Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
class	SamFormatConverter Converts a BAM file to human-readable SAM output or vice versa
class	SamToFastq Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format.
class	SetNmAndUqTags
class	SortSam
class	SplitSamByLibrary Command-line program to split a SAM or BAM file into separate files based on library name.
class	ValidateSamFile Command line program wrapping SamFileValidator.
class	ViewSam Very simple command that just reads a SAM or BAM file and writes out the header and each records to standard out.

Uses of CommandLineProgram in picard.sam.markduplicates

Subclasses of CommandLineProgram in picard.sam.markduplicates

Modifier and Type	Class and Description
class	EstimateLibraryComplexity Attempts to estimate library complexity from sequence alone.
class	MarkDuplicates A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
class	MarkDuplicatesWithMateCigar An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.

Uses of CommandLineProgram in picard.sam.markduplicates.util

Subclasses of CommandLineProgram in picard.sam.markduplicates.util

Modifier and Type	Class and Description
class	AbstractMarkDuplicatesCommandLineProgram Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM files.
class	AbstractOpticalDuplicateFinderCommandLineProgram Abstract class that holds parameters and methods common to classes that optical duplicate detection.

Uses of CommandLineProgram in picard.util

Subclasses of CommandLineProgram in picard.util

Modifier and Type	Class and Description
class	BaitDesigner Designs baits for hybrid selection!
class	BedToIntervalList
class	FifoBuffer A program that is designed to act as a large memory buffer between processes that are connected with unix pipes where one or more processes either produce or consume their input or output in bursts.
class	IntervalListToBed Trivially simple command line program to convert an IntervalList file to a BED file.
class	IntervalListTools Little class to aid working with interval lists.
class	LiftOverIntervalList
class	ScatterIntervalsByNs A CLP for breaking up a reference into intervals of Ns and ACGTs bases.

Uses of CommandLineProgram in picard.vcf

Subclasses of CommandLineProgram in picard.vcf

Modifier and Type	Class and Description
class	CollectVariantCallingMetrics Collects summary and per-sample metrics about variant calls in a VCF file.
class	GatherVcfs Simple little class that combines multiple VCFs that have exactly the same set of samples and totally discrete sets of loci.
class	GenotypeConcordance Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference) the other being the call.
class	LiftoverVcf Tool for lifting over a VCF to another genome build and producing a properly header'd, sorted and indexed VCF in one go.
class	MakeSitesOnlyVcf Writes out a VCF that contains all the site-level information for all records in the input VCF and no per-sample information.
class	MergeVcfs Combines multiple VCF files into a single file.
class	RenameSampleInVcf
class	SortVcf Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
class	SplitVcfs Splits the input VCF file into two, one for indels and one for SNPs.
class	UpdateVcfSequenceDictionary Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
class	VcfFormatConverter Converts an ASCII VCF file to a binary BCF or vice versa.
class	VcfToIntervalList Creates an interval list from a VCF

Uses of CommandLineProgram in picard.vcf.filter

Subclasses of CommandLineProgram in picard.vcf.filter

Modifier and Type	Class and Description
class	FilterVcf Applies a set of hard filters to Variants and to Genotypes within a VCF.