Package picard.analysis.artifacts
Class CollectSequencingArtifactMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.analysis.artifacts.CollectSequencingArtifactMetrics
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@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
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Field Summary
Fields Modifier and Type Field Description int
CONTEXT_SIZE
Set<String>
CONTEXTS_TO_PRINT
File
DB_SNP
String
FILE_EXTENSION
boolean
INCLUDE_DUPLICATES
boolean
INCLUDE_NON_PF_READS
boolean
INCLUDE_UNPAIRED
File
INTERVALS
int
MAXIMUM_INSERT_SIZE
int
MINIMUM_INSERT_SIZE
int
MINIMUM_MAPPING_QUALITY
int
MINIMUM_QUALITY_SCORE
boolean
TANDEM_READS
static String
USAGE_SUMMARY
boolean
USE_OQ
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Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, output, OUTPUT, STOP_AFTER
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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
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Constructor Summary
Constructors Constructor Description CollectSequencingArtifactMetrics()
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Method Summary
All 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 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, 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, getOutputArgumentCollection, makeItSo, setReferenceSequence
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Detail
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USAGE_SUMMARY
public static final String USAGE_SUMMARY
- See Also:
- Constant Field Values
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INTERVALS
@Argument(doc="An optional list of intervals to restrict analysis to.", optional=true) public File INTERVALS
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DB_SNP
@Argument(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.", optional=true) public File DB_SNP
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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
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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
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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
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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
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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
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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
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INCLUDE_NON_PF_READS
@Argument(shortName="NON_PF", doc="Whether or not to include non-PF reads.") public boolean INCLUDE_NON_PF_READS
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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
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USE_OQ
@Argument(doc="When available, use original quality scores for filtering.") public boolean USE_OQ
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CONTEXT_SIZE
@Argument(doc="The number of context bases to include on each side of the assayed base.") public int CONTEXT_SIZE
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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 Set<String> 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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Method Detail
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requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
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customCommandLineValidation
protected 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 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
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 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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