| Interface | Description |
|---|---|
| CollectMultipleMetrics.ProgramInterface |
| Class | Description |
|---|---|
| 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.
|
| 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
|
| 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.
|
| CollectWgsMetrics |
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
|
| CollectWgsMetrics.WgsMetrics |
Metrics for evaluating the performance of whole genome sequencing experiments.
|
| CollectWgsMetricsFromQuerySorted | Deprecated |
| CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics |
Metrics for evaluating the performance of whole genome sequencing experiments.
|
| CollectWgsMetricsFromSampledSites | Deprecated |
| CollectWgsMetricsFromSampledSites.SampledWgsMetrics | |
| CollectWgsMetricsWithNonZeroCoverage | |
| CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage |
Metrics for evaluating the performance of whole genome sequencing experiments.
|
| CompareMetrics |
Compare two metrics files.
|
| 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.
|
| 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 |
| Enum | Description |
|---|---|
| AlignmentSummaryMetrics.Category | |
| CollectMultipleMetrics.Program | |
| CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY |
the various metrics types
|
| CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category | |
| MetricAccumulationLevel |
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
|