Package picard.vcf
Class MakeSitesOnlyVcf
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.MakeSitesOnlyVcf
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
Summary
This tool reads a VCF/VCF.gz/BCF and removes all genotype information from it while retaining all site level information, including annotations based on genotypes (e.g. AN, AF). Output can be any supported variant format including .vcf, .vcf.gz or .bcf.Inputs
- Input VCF or BCF file containing genotype and site-level information.
- Output VCF or BCF file containing only site-level information.
- [Optional] Names of one or more samples to include in the output VCF.
Usage example:
java -jar picard.jar MakeSitesOnlyVcf \ INPUT=input_variants.vcf \ OUTPUT=output_variants.vcf
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Field Summary
FieldsFields 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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Constructor Details
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MakeSitesOnlyVcf
public MakeSitesOnlyVcf()
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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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