picard.analysis

Class CollectGcBiasMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.analysis.CollectGcBiasMetrics

@DocumentedFeature
public class CollectGcBiasMetrics
extends SinglePassSamProgram

Tool to collect information about GC bias in the reads in a given BAM file. Computes the number of windows (of size specified by SCAN_WINDOW_SIZE) in the genome at each GC% and counts the number of read starts in each GC bin. What is output and plotted is the "normalized coverage" in each bin - i.e. the number of reads per window normalized to the average number of reads per window across the whole genome.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ALSO_IGNORE_DUPLICATES
java.io.File	CHART_OUTPUT
boolean	IS_BISULFITE_SEQUENCED
java.util.Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
double	MINIMUM_GENOME_FRACTION
int	SCAN_WINDOW_SIZE
java.io.File	SUMMARY_OUTPUT

Fields inherited from class picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, output, OUTPUT, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, 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
CollectGcBiasMetrics()

Method Summary

Modifier and Type	Method and Description
protected void	acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.
protected void	finish() Should be implemented by subclasses to do one-time finalization work.
protected void	setup(htsjdk.samtools.SAMFileHeader header, java.io.File samFile) Should be implemented by subclasses to do one-time initialization work.

Methods inherited from class picard.analysis.SinglePassSamProgram

doWork, getOutputArgumentCollection, makeItSo, setReferenceSequence, usesNoRefReads

Methods inherited from class picard.cmdline.CommandLineProgram

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

Methods inherited from class java.lang.Object

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

Field Detail

CHART_OUTPUT

@Argument(shortName="CHART",
          doc="The PDF file to render the chart to.")
public java.io.File CHART_OUTPUT

SUMMARY_OUTPUT

@Argument(shortName="S",
          doc="The text file to write summary metrics to.")
public java.io.File SUMMARY_OUTPUT

SCAN_WINDOW_SIZE

@Argument(shortName="WINDOW_SIZE",
          doc="The size of the scanning windows on the reference genome that are used to bin reads.")
public int SCAN_WINDOW_SIZE

MINIMUM_GENOME_FRACTION

@Argument(shortName="MGF",
          doc="For summary metrics, exclude GC windows that include less than this fraction of the genome.")
public double MINIMUM_GENOME_FRACTION

IS_BISULFITE_SEQUENCED

@Argument(shortName="BS",
          doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.")
public boolean IS_BISULFITE_SEQUENCED

METRIC_ACCUMULATION_LEVEL

@Argument(shortName="LEVEL",
          doc="The level(s) at which to accumulate metrics.")
public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

ALSO_IGNORE_DUPLICATES

@Argument(shortName="ALSO_IGNORE_DUPLICATES",
          doc="Use to get additional results without duplicates. This option allows to gain two plots per level at the same time: one is the usual one and the other excludes duplicates.")
public boolean ALSO_IGNORE_DUPLICATES

Constructor Detail

CollectGcBiasMetrics

public CollectGcBiasMetrics()

Method Detail

setup

protected void setup(htsjdk.samtools.SAMFileHeader header,
                     java.io.File samFile)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time initialization work.

Specified by:

setup in class SinglePassSamProgram

acceptRead

protected void acceptRead(htsjdk.samtools.SAMRecord rec,
                          htsjdk.samtools.reference.ReferenceSequence ref)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.

Specified by:

acceptRead in class SinglePassSamProgram

finish

protected void finish()

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time finalization work.

Specified by:

finish in class SinglePassSamProgram