Package picard.vcf
Class MakeSitesOnlyVcf
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.vcf.MakeSitesOnlyVcf
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@DocumentedFeature public class MakeSitesOnlyVcf extends CommandLineProgram
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
Fields Modifier and Type Field Description File
INPUT
File
OUTPUT
Set<String>
SAMPLE
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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 MakeSitesOnlyVcf()
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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
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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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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