Package picard.analysis

Interface Summary

Interface	Description
CollectMultipleMetrics.ProgramInterface
WgsMetricsProcessor	Interface for processing data and generate result for CollectWgsMetrics

Class Summary

Class	Description
AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset>	Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
AdapterUtility	A utility class for matching reads to adapters.
AlignmentSummaryMetrics	High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
AlignmentSummaryMetricsCollector
BaseDistributionByCycleMetrics
ChimeraUtil
CollectAlignmentSummaryMetrics	A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectBaseDistributionByCycle
CollectGcBiasMetrics	Tool to collect information about GC bias in the reads in a given BAM file.
CollectInsertSizeMetrics	Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
CollectJumpingLibraryMetrics	Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
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.
CollectOxoGMetrics	Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics.CpcgMetrics	Metrics class for outputs.
CollectQualityYieldMetrics	Command line program to calibrate quality yield metrics
CollectQualityYieldMetrics.QualityYieldMetrics	A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetricsCollector
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.
CollectRawWgsMetrics.RawWgsMetrics
CollectRnaSeqMetrics
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.
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectWgsMetrics	Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetrics.WgsMetricsCollector
CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage	Metrics for evaluating the performance of whole genome sequencing experiments.
CompareMetrics	Compare two metrics files.
CounterManager	Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
FastWgsMetricsCollector	Class represents fast algorithm for collecting data from AbstractLocusInfo with a list of aligned EdgingRecordAndOffset objects.
FingerprintingDetailMetrics	Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
FingerprintingSummaryMetrics	Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
GcBiasDetailMetrics	Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
GcBiasMetricsCollector	Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
GcBiasSummaryMetrics	High level metrics that capture how biased the coverage in a certain lane is.
GcBiasUtils	Utilities to calculate GC Bias Created by kbergin on 9/23/15.
InsertSizeMetrics	Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
JumpingLibraryMetrics	High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
MeanQualityByCycle	Program to generate a data table and chart of mean quality by cycle from a BAM file.
MergeableMetricBase	An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (MergeByAdding).
QualityScoreDistribution	Charts quality score distribution within a BAM file.
RnaSeqMetrics	Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
RrbsCpgDetailMetrics	Holds information about CpG sites encountered for RRBS processing QC
RrbsMetricsCollector
RrbsSummaryMetrics	Holds summary statistics from RRBS processing QC
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.
TheoreticalSensitivity	Created by David Benjamin on 5/13/15.
TheoreticalSensitivity.RouletteWheel
TheoreticalSensitivityMetrics	TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
WgsMetrics	Metrics for evaluating the performance of whole genome sequencing experiments.
WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>	Implementation of WgsMetricsProcessor that gets input data from a given iterator and processes it with a help of collector

Enum Summary

Enum	Description
AlignmentSummaryMetrics.Category
CollectMultipleMetrics.Program
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
MetricAccumulationLevel	For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.

Annotation Types Summary

Annotation Type	Description
MergeableMetricBase.MergeByAdding	Metrics whose values can be merged by adding.
MergeableMetricBase.MergeByAssertEquals	Metrics whose values should be equal when merging.
MergeableMetricBase.MergingIsManual	Metrics that are merged manually in the MergeableMetricBase.merge(MergeableMetricBase) ()}.
MergeableMetricBase.NoMergingIsDerived	Metrics that are not merged, but are subsequently derived from other metrics, for example by MergeableMetricBase.calculateDerivedFields().
MergeableMetricBase.NoMergingKeepsValue	Metrics that are not merged.