Package picard.vcf
Class SplitVcfs
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.vcf.SplitVcfs
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@DocumentedFeature public class SplitVcfs extends CommandLineProgram
Splits the input VCF file into two, one for indels and one for SNPs. The headers of the two output files will be identical. An index file is created for the output file by default. Using an output file name with a ".gz" extension will create gzip-compressed output.
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Field Summary
Fields Modifier and Type Field Description File
INDEL_OUTPUT
PicardHtsPath
INPUT
PicardHtsPath
SEQUENCE_DICTIONARY
File
SNP_OUTPUT
Boolean
STRICT
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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 SplitVcfs()
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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="The VCF or BCF input file") public PicardHtsPath INPUT
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SNP_OUTPUT
@Argument(doc="The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.") public File SNP_OUTPUT
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INDEL_OUTPUT
@Argument(doc="The VCF or BCF file to which indel records should be written. The file format is determined by file extension.") public File INDEL_OUTPUT
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SEQUENCE_DICTIONARY
@Argument(shortName="D", doc="The index sequence dictionary to use instead of the sequence dictionaries in the input files", optional=true) public PicardHtsPath SEQUENCE_DICTIONARY
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STRICT
@Argument(doc="If true an exception will be thrown if an event type other than SNP or indel is encountered") public Boolean STRICT
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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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