picard.analysis

Class CollectWgsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectWgsMetrics

Direct Known Subclasses:

CollectRawWgsMetrics, CollectWgsMetricsFromSampledSites, CollectWgsMetricsWithNonZeroCoverage

public class CollectWgsMetrics
extends CommandLineProgram

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

Author:

tfennell

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.
protected 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
java.io.File	INTERVALS
int	LOCUS_ACCUMULATION_CAP
int	MINIMUM_BASE_QUALITY
int	MINIMUM_MAPPING_QUALITY
java.io.File	OUTPUT
java.io.File	REFERENCE_SEQUENCE
int	SAMPLE_SIZE
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

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
protected CollectWgsMetrics.WgsMetrics	generateWgsMetrics()
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 CollectWgsMetrics.WgsMetricsCollector	getCollector(int coverageCap)
protected htsjdk.samtools.util.SamLocusIterator	getLocusIterator(htsjdk.samtools.SamReader in)
protected htsjdk.samtools.SAMFileHeader	getSamFileHeader()
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 positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).",
        overridable=true)
public int COVERAGE_CAP

LOCUS_ACCUMULATION_CAP

@Option(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",
        overridable=true)
public int LOCUS_ACCUMULATION_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

COUNT_UNPAIRED

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

SAMPLE_SIZE

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

INTERVALS

@Option(doc="An interval list file that contains the positions to restrict the assessment. Please note that all bases of reads that overlap these intervals will be considered, even if some of those bases extend beyond the boundaries of the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs. To restrict the calculation just to individual positions without overlap, please see CollectWgsMetricsFromSampledSites.",
        optional=true,
        overridable=true)
public java.io.File INTERVALS

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.

getSamFileHeader

protected htsjdk.samtools.SAMFileHeader getSamFileHeader()

generateWgsMetrics

protected CollectWgsMetrics.WgsMetrics generateWgsMetrics()

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.SamLocusIterator getLocusIterator(htsjdk.samtools.SamReader in)

getCollector

protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap)