picard.analysis.artifacts

Class CollectSequencingArtifactMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.analysis.artifacts.CollectSequencingArtifactMetrics

@DocumentedFeature
public class CollectSequencingArtifactMetrics
extends SinglePassSamProgram

Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep. We measure two distinct error types - artifacts that are introduced before the addition of the read1/read2 adapters ("pre adapter") and those that are introduced after target selection ("bait bias"). For each of these, we provide summary metrics as well as detail metrics broken down by reference context (the ref bases surrounding the substitution event). For a deeper explanation, see Costello et al. 2013: http://www.ncbi.nlm.nih.gov/pubmed/23303777

Field Summary

Fields

Modifier and Type	Field and Description
int	CONTEXT_SIZE
java.util.Set<java.lang.String>	CONTEXTS_TO_PRINT
java.io.File	DB_SNP
java.lang.String	FILE_EXTENSION
boolean	INCLUDE_DUPLICATES
boolean	INCLUDE_NON_PF_READS
boolean	INCLUDE_UNPAIRED
java.io.File	INTERVALS
int	MAXIMUM_INSERT_SIZE
int	MINIMUM_INSERT_SIZE
int	MINIMUM_MAPPING_QUALITY
int	MINIMUM_QUALITY_SCORE
boolean	TANDEM_READS
boolean	USE_OQ

Fields inherited from class picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, 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
CollectSequencingArtifactMetrics()

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 java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected void	finish() Should be implemented by subclasses to do one-time finalization work.
protected boolean	requiresReference()
protected void	setup(htsjdk.samtools.SAMFileHeader header, java.io.File samFile) Should be implemented by subclasses to do one-time initialization work.
protected boolean	usesNoRefReads() Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.

Methods inherited from class picard.analysis.SinglePassSamProgram

doWork, makeItSo, setReferenceSequence

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, 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

INTERVALS

@Argument(doc="An optional list of intervals to restrict analysis to.",
          optional=true)
public java.io.File INTERVALS

DB_SNP

@Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.",
          optional=true)
public java.io.File DB_SNP

MINIMUM_QUALITY_SCORE

@Argument(shortName="Q",
          doc="The minimum base quality score for a base to be included in analysis.")
public int MINIMUM_QUALITY_SCORE

MINIMUM_MAPPING_QUALITY

@Argument(shortName="MQ",
          doc="The minimum mapping quality score for a base to be included in analysis.")
public int MINIMUM_MAPPING_QUALITY

MINIMUM_INSERT_SIZE

@Argument(shortName="MIN_INS",
          doc="The minimum insert size for a read to be included in analysis.")
public int MINIMUM_INSERT_SIZE

MAXIMUM_INSERT_SIZE

@Argument(shortName="MAX_INS",
          doc="The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.")
public int MAXIMUM_INSERT_SIZE

INCLUDE_UNPAIRED

@Argument(shortName="UNPAIRED",
          doc="Include unpaired reads. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.")
public boolean INCLUDE_UNPAIRED

INCLUDE_DUPLICATES

@Argument(shortName="DUPES",
          doc="Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.")
public boolean INCLUDE_DUPLICATES

INCLUDE_NON_PF_READS

@Argument(shortName="NON_PF",
          doc="Whether or not to include non-PF reads.")
public boolean INCLUDE_NON_PF_READS

TANDEM_READS

@Argument(shortName="TANDEM",
          doc="Set to true if mate pairs are being sequenced from the same strand, i.e. they\'re expected to face the same direction.")
public boolean TANDEM_READS

USE_OQ

@Argument(doc="When available, use original quality scores for filtering.")
public boolean USE_OQ

CONTEXT_SIZE

@Argument(doc="The number of context bases to include on each side of the assayed base.")
public int CONTEXT_SIZE

CONTEXTS_TO_PRINT

@Argument(doc="If specified, only print results for these contexts in the detail metrics output. However, the summary metrics output will still take all contexts into consideration.",
          optional=true)
public java.util.Set<java.lang.String> CONTEXTS_TO_PRINT

FILE_EXTENSION

@Argument(shortName="EXT",
          doc="Append the given file extension to all metric file names (ex. OUTPUT.pre_adapter_summary_metrics.EXT). None if null",
          optional=true)
public java.lang.String FILE_EXTENSION

Constructor Detail

CollectSequencingArtifactMetrics

public CollectSequencingArtifactMetrics()

Method Detail

requiresReference

protected boolean requiresReference()

Overrides:

requiresReference in class CommandLineProgram

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

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

usesNoRefReads

protected boolean usesNoRefReads()

Description copied from class: SinglePassSamProgram

Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.

Overrides:

usesNoRefReads in class SinglePassSamProgram