Package picard.analysis.artifacts
Class CollectSequencingArtifactMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.analysis.artifacts.CollectSequencingArtifactMetrics
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
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Field Summary
FieldsModifier and TypeFieldDescriptionint
boolean
boolean
boolean
int
int
int
int
boolean
static final String
boolean
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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
acceptRead
(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.protected String[]
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
protected void
Should be implemented by subclasses to do one-time initialization work.protected boolean
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, getOutputArgumentCollection, makeItSo, setReferenceSequence
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Details
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USAGE_SUMMARY
- See Also:
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INTERVALS
@Argument(doc="An optional list of intervals to restrict analysis to.", optional=true) public File INTERVALS -
DB_SNP
@Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.", optional=true) public 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
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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 String FILE_EXTENSION
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Constructor Details
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CollectSequencingArtifactMetrics
public CollectSequencingArtifactMetrics()
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Method Details
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requiresReference
protected boolean requiresReference()- Overrides:
requiresReference
in classCommandLineProgram
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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 classCommandLineProgram
- 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.
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setup
Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to do one-time initialization work.- Specified by:
setup
in classSinglePassSamProgram
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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 classSinglePassSamProgram
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finish
protected void finish()Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to do one-time finalization work.- Specified by:
finish
in classSinglePassSamProgram
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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 classSinglePassSamProgram
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