Package picard.arrays
Class MergePedIntoVcf
java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.MergePedIntoVcf
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
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Field Summary
FieldsModifier and TypeFieldDescriptionFields 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, 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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ORIGINAL_VCF
@Argument(shortName="VCF", doc="The vcf containing the original autocall genotypes.") public File ORIGINAL_VCF -
PED_FILE
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MAP_FILE
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ZCALL_THRESHOLDS_FILE
@Argument(shortName="ZCALL_T_FILE", doc="The zcall thresholds file.") public File ZCALL_THRESHOLDS_FILE -
ZCALL_VERSION
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OUTPUT
@Argument(shortName="O", doc="The output VCF file to write with merged genotype calls.") public File OUTPUT
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Constructor Details
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MergePedIntoVcf
public MergePedIntoVcf()
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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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