picard.analysis

Class CollectWgsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectWgsMetrics

Direct Known Subclasses:

CollectRawWgsMetrics, CollectWgsMetricsWithNonZeroCoverage

@DocumentedFeature
public class CollectWgsMetrics
extends CommandLineProgram

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. Two algorithms are available for this metrics: default and fast. The fast algorithm is enabled by USE_FAST_ALGORITHM option. The fast algorithm works better for regions of BAM file with coverage at least 10 reads per locus, for lower coverage the algorithms perform the same.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
static class	CollectWgsMetrics.WgsMetrics Metrics for evaluating the performance of whole genome sequencing experiments.
protected static class	CollectWgsMetrics.WgsMetricsCollector

Field Summary

Fields

Modifier and Type	Field and Description
boolean	COUNT_UNPAIRED
int	COVERAGE_CAP
boolean	INCLUDE_BQ_HISTOGRAM
java.io.File	INPUT
protected IntervalArgumentCollection	intervalArugmentCollection
protected java.io.File	INTERVALS
int	LOCUS_ACCUMULATION_CAP
int	MINIMUM_BASE_QUALITY
int	MINIMUM_MAPPING_QUALITY
java.io.File	OUTPUT
int	READ_LENGTH
int	SAMPLE_SIZE
long	STOP_AFTER
boolean	USE_FAST_ALGORITHM

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectWgsMetrics()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
protected CollectWgsMetrics.WgsMetrics	generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram, int theoreticalHetSensitivitySampleSize)
protected long	getBasesExcludedBy(CountingFilter filter) If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge.
protected AbstractWgsMetricsCollector	getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals) Creates AbstractWgsMetricsCollector implementation according to this#USE_FAST_ALGORITHM value.
protected htsjdk.samtools.util.IntervalList	getIntervalsToExamine() Gets the intervals over which we will calculate metrics.
protected htsjdk.samtools.util.AbstractLocusIterator	getLocusIterator(htsjdk.samtools.SamReader in) Creates AbstractLocusIterator implementation according to this#USE_FAST_ALGORITHM value.
protected htsjdk.samtools.SAMFileHeader	getSamFileHeader() This method should only be called after this.getSamReader() is called.
protected htsjdk.samtools.SamReader	getSamReader() Gets the SamReader from which records will be examined.
static void	main(java.lang.String[] args)
protected IntervalArgumentCollection	makeIntervalArgumentCollection()
protected boolean	requiresReference()

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Argument(shortName="I",
          doc="Input SAM or BAM file.")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output metrics file.")
public java.io.File OUTPUT

MINIMUM_MAPPING_QUALITY

@Argument(shortName="MQ",
          doc="Minimum mapping quality for a read to contribute coverage.")
public int MINIMUM_MAPPING_QUALITY

MINIMUM_BASE_QUALITY

@Argument(shortName="Q",
          doc="Minimum base quality for a base to contribute coverage. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter.")
public int MINIMUM_BASE_QUALITY

COVERAGE_CAP

@Argument(shortName="CAP",
          doc="Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).")
public int COVERAGE_CAP

LOCUS_ACCUMULATION_CAP

@Argument(doc="At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED).  Used to keep memory consumption in check, but could create bias if set too low")
public int LOCUS_ACCUMULATION_CAP

STOP_AFTER

@Argument(doc="For debugging purposes, stop after processing this many genomic bases.")
public long STOP_AFTER

INCLUDE_BQ_HISTOGRAM

@Argument(doc="Determines whether to include the base quality histogram in the metrics file.")
public boolean INCLUDE_BQ_HISTOGRAM

COUNT_UNPAIRED

@Argument(doc="If true, count unpaired reads, and paired reads with one end unmapped")
public boolean COUNT_UNPAIRED

SAMPLE_SIZE

@Argument(doc="Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.",
          optional=true)
public int SAMPLE_SIZE

intervalArugmentCollection

@ArgumentCollection
protected IntervalArgumentCollection intervalArugmentCollection

USE_FAST_ALGORITHM

@Argument(doc="If true, fast algorithm is used.")
public boolean USE_FAST_ALGORITHM

READ_LENGTH

@Argument(doc="Average read length in the file. Default is 150.",
          optional=true)
public int READ_LENGTH

INTERVALS

protected java.io.File INTERVALS

Constructor Detail

CollectWgsMetrics

public CollectWgsMetrics()

Method Detail

requiresReference

protected boolean requiresReference()

Overrides:

requiresReference in class CommandLineProgram

makeIntervalArgumentCollection

protected IntervalArgumentCollection makeIntervalArgumentCollection()

Returns:

An interval argument collection to be used for this tool. Subclasses can override this to provide an argument collection with alternative arguments or argument annotations.

main

public static void main(java.lang.String[] args)

getSamReader

protected htsjdk.samtools.SamReader getSamReader()

Gets the SamReader from which records will be examined. This will also set the header so that it is available in

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

getIntervalsToExamine

protected htsjdk.samtools.util.IntervalList getIntervalsToExamine()

Gets the intervals over which we will calculate metrics.

getSamFileHeader

protected htsjdk.samtools.SAMFileHeader getSamFileHeader()

This method should only be called after this.getSamReader() is called.

generateWgsMetrics

protected CollectWgsMetrics.WgsMetrics generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals,
                                                          htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram,
                                                          htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram,
                                                          double pctExcludedByMapq,
                                                          double pctExcludedByDupes,
                                                          double pctExcludedByPairing,
                                                          double pctExcludedByBaseq,
                                                          double pctExcludedByOverlap,
                                                          double pctExcludedByCapping,
                                                          double pctTotal,
                                                          int coverageCap,
                                                          htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram,
                                                          int theoreticalHetSensitivitySampleSize)

getBasesExcludedBy

protected long getBasesExcludedBy(CountingFilter filter)

If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge. Ideally INTERVALS should only include regions that have hard edges without reads that could extend beyond the boundary (such as a whole contig).

getLocusIterator

protected htsjdk.samtools.util.AbstractLocusIterator getLocusIterator(htsjdk.samtools.SamReader in)

Creates AbstractLocusIterator implementation according to this#USE_FAST_ALGORITHM value.

Parameters:

in - inner SamReader

Returns:

if this#USE_FAST_ALGORITHM is enabled, returns EdgeReadIterator implementation, otherwise default algorithm is used and SamLocusIterator is returned.

getCollector

protected AbstractWgsMetricsCollector getCollector(int coverageCap,
                                                   htsjdk.samtools.util.IntervalList intervals)

Creates AbstractWgsMetricsCollector implementation according to this#USE_FAST_ALGORITHM value.

Parameters:

coverageCap - the maximum depth/coverage to consider.

intervals - the intervals over which metrics are collected.

Returns:

if this#USE_FAST_ALGORITHM is enabled, returns FastWgsMetricsCollector implementation, otherwise default algorithm is used and CollectWgsMetrics.WgsMetricsCollector is returned.