Package picard.vcf
Class CollectVariantCallingMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.CollectVariantCallingMetrics
Collects summary and per-sample metrics about variant calls in a VCF file.
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.static class
A collection of metrics relating to snps and indels within a variant-calling file (VCF). -
Field Summary
FieldsModifier and TypeFieldDescriptionboolean
int
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, 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 int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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INPUT
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OUTPUT
@Argument(shortName="O", doc="Path (except for the file extension) of output metrics files to write.") public File OUTPUT -
DBSNP
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TARGET_INTERVALS
@Argument(shortName="TI", doc="Target intervals to restrict analysis to.", optional=true) public PicardHtsPath TARGET_INTERVALS -
SEQUENCE_DICTIONARY
@Argument(shortName="SD", optional=true, doc="If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.") public PicardHtsPath SEQUENCE_DICTIONARY -
GVCF_INPUT
@Argument(doc="Set to true if running on a single-sample gvcf.", optional=true) public boolean GVCF_INPUT -
THREAD_COUNT
@Argument public int THREAD_COUNT
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Constructor Details
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CollectVariantCallingMetrics
public CollectVariantCallingMetrics()
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Method Details
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doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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