# Package picard.analysis

package picard.analysis

Related Packages
Package
Description
picard
picard.analysis.artifacts
picard.analysis.directed
picard.analysis.replicates
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".
AlignmentSummaryMetrics.Category
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.
CollectMultipleMetrics.Program
CollectMultipleMetrics.ProgramInterface
CollectOxoGMetrics
Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics.CpcgMetrics
Metrics class for outputs.
CollectQualityYieldMetrics
Command line program to calculate quality yield metrics
CollectQualityYieldMetrics.QualityYieldMetrics
A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetricsCollector
CollectQualityYieldMetricsFlow
Command line program to calculate quality yield metrics for flow based read files
CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetricsSNVQ
Command line program to calculate SNV quality yield metrics for read files
CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
A set of metrics used to describe the general quality of a BAM file
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
CollectUmiPrevalenceMetrics
A CLP that, tallies the number of UMIs in a duplicate set across the entire bam and produces a histogram.
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.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CompareMetrics
Compare two metrics files.
CompareMetrics.MetricComparisonDifferences
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`).
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.
MetricAccumulationLevel
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
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.
WgsMetricsProcessor
Interface for processing data and generate result for CollectWgsMetrics
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