Package picard.vcf
Class CollectVariantCallingMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.vcf.CollectVariantCallingMetrics
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@DocumentedFeature public class CollectVariantCallingMetrics extends CommandLineProgram
Collects summary and per-sample metrics about variant calls in a VCF file.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectVariantCallingMetrics.VariantCallingDetailMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.static class
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
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Field Summary
Fields Modifier and Type Field Description File
DBSNP
boolean
GVCF_INPUT
File
INPUT
File
OUTPUT
File
SEQUENCE_DICTIONARY
File
TARGET_INTERVALS
int
THREAD_COUNT
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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 CollectVariantCallingMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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 Detail
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INPUT
@Argument(shortName="I", doc="Input vcf file for analysis") public File 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
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DBSNP
@Argument(doc="Reference dbSNP file in dbSNP or VCF format.") public File DBSNP
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TARGET_INTERVALS
@Argument(shortName="TI", doc="Target intervals to restrict analysis to.", optional=true) public File TARGET_INTERVALS
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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 File SEQUENCE_DICTIONARY
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GVCF_INPUT
@Argument(doc="Set to true if running on a single-sample gvcf.", optional=true) public boolean GVCF_INPUT
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THREAD_COUNT
@Argument public int THREAD_COUNT
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Method Detail
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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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