picard.analysis

Class CollectWgsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectWgsMetrics

Direct Known Subclasses:

CollectRawWgsMetrics

public class CollectWgsMetrics
extends CommandLineProgram

Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field and Description
int	COVERAGE_CAP
boolean	INCLUDE_BQ_HISTOGRAM
java.io.File	INPUT
int	MINIMUM_BASE_QUALITY
int	MINIMUM_MAPPING_QUALITY
java.io.File	OUTPUT
java.io.File	REFERENCE_SEQUENCE
long	STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectWgsMetrics()

Method Summary

Methods

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
protected CollectWgsMetrics.WgsMetrics	generateWgsMetrics()
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

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

OUTPUT

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

REFERENCE_SEQUENCE

@Option(shortName="R",
        doc="The reference sequence fasta aligned to.")
public java.io.File REFERENCE_SEQUENCE

MINIMUM_MAPPING_QUALITY

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

MINIMUM_BASE_QUALITY

@Option(shortName="Q",
        doc="Minimum base quality for a base to contribute coverage.",
        overridable=true)
public int MINIMUM_BASE_QUALITY

COVERAGE_CAP

@Option(shortName="CAP",
        doc="Treat bases with coverage exceeding this value as if they had coverage at this value.",
        overridable=true)
public int COVERAGE_CAP

STOP_AFTER

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

INCLUDE_BQ_HISTOGRAM

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

Constructor Detail

CollectWgsMetrics

public CollectWgsMetrics()

Method Detail

main

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

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.

generateWgsMetrics

protected CollectWgsMetrics.WgsMetrics generateWgsMetrics()