| Package | Description |
|---|---|
| picard.analysis | |
| picard.analysis.artifacts | |
| picard.analysis.directed | |
| picard.metrics |
| Class and Description |
|---|
| 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 |
| CollectMultipleMetrics.Program |
| CollectMultipleMetrics.ProgramInterface |
| 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.
|
| CollectWgsMetrics.WgsMetricsCollector |
| CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
Deprecated.
the various metrics types
|
| CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
Metrics for evaluating the performance of whole genome sequencing experiments.
|
| CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category |
| MetricAccumulationLevel
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
|
| 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.
|
| Class and Description |
|---|
| 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.
|
| Class and Description |
|---|
| 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".
|
| MetricAccumulationLevel
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
|
| 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".
|
| Class and Description |
|---|
| GcBiasDetailMetrics
Class that holds detailed metrics about reads that fall within windows of a certain
GC bin on the reference genome.
|
| GcBiasSummaryMetrics
High level metrics that capture how biased the coverage in a certain lane is.
|
| MetricAccumulationLevel
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
|