CollectGcBiasMetrics (picard 2.18.2 API)

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	Description
`boolean`	`ALSO_IGNORE_DUPLICATES`
`File`	`CHART_OUTPUT`
`boolean`	`IS_BISULFITE_SEQUENCED`
`Set<MetricAccumulationLevel>`	`METRIC_ACCUMULATION_LEVEL`
`double`	`MINIMUM_GENOME_FRACTION`
`int`	`SCAN_WINDOW_SIZE`
`File`	`SUMMARY_OUTPUT`

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

Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER

Constructor Summary

Constructors
Constructor Description

CollectGcBiasMetrics()

Constructors
Constructor	Description
`CollectGcBiasMetrics()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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.
`static void`	`main(String[] args)`
`protected void`	`setup(htsjdk.samtools.SAMFileHeader header, File samFile)`	Should be implemented by subclasses to do one-time initialization work.

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, 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

Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, makeItSo, setReferenceSequence, usesNoRefReads

Field Detail

CHART_OUTPUT

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

SUMMARY_OUTPUT

@Argument(shortName="S",
          doc="The text file to write summary metrics to.")
public 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 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
- main
```
public static void main(String[] args)
```
- setup
```
protected void setup(htsjdk.samtools.SAMFileHeader header,
                     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

Class CollectGcBiasMetrics

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Fields inherited from class picard.analysis.SinglePassSamProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Methods inherited from class picard.analysis.SinglePassSamProgram

Field Detail

CHART_OUTPUT

SUMMARY_OUTPUT

SCAN_WINDOW_SIZE

MINIMUM_GENOME_FRACTION

IS_BISULFITE_SEQUENCED

METRIC_ACCUMULATION_LEVEL

ALSO_IGNORE_DUPLICATES

Constructor Detail

CollectGcBiasMetrics

Method Detail

main

setup

acceptRead

finish