Package picard.analysis
package picard.analysis
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ClassDescriptionAbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset>Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.A utility class for matching reads to adapters.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".A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.Tool to collect information about GC bias in the reads in a given BAM file.Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.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 for trying to quantify the CpCG->CpCA error rate.Metrics class for outputs.Command line program to calculate quality yield metricsA set of metrics used to describe the general quality of a BAM fileComputes 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.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.Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.Metrics for evaluating the performance of whole genome sequencing experiments.Compare two metrics files.Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.Class represents fast algorithm for collecting data fromAbstractLocusInfo
with a list of alignedEdgingRecordAndOffset
objects.Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.High level metrics that capture how biased the coverage in a certain lane is.Utilities to calculate GC Bias Created by kbergin on 9/23/15.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".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".Program to generate a data table and chart of mean quality by cycle from a BAM file.An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (MergeByAdding
).Metrics whose values can be merged by adding.Metrics whose values should be equal when merging.Metrics that are merged manually in theMergeableMetricBase.merge(MergeableMetricBase)
()}.Metrics that are not merged, but are subsequently derived from other metrics, for example byMergeableMetricBase.calculateDerivedFields()
.Metrics that are not merged.For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.Charts quality score distribution within a BAM file.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".Holds information about CpG sites encountered for RRBS processing QCHolds summary statistics from RRBS processing QCSuper 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.Created by David Benjamin on 5/13/15.TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.Metrics for evaluating the performance of whole genome sequencing experiments.Interface for processing data and generate result for CollectWgsMetricsWgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>Implementation ofWgsMetricsProcessor
that gets input data from a given iterator and processes it with a help of collector