Package picard.arrays
Class MergePedIntoVcf
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.arrays.MergePedIntoVcf
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@DocumentedFeature public class MergePedIntoVcf extends CommandLineProgram
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
Fields Modifier and Type Field Description File
MAP_FILE
File
ORIGINAL_VCF
File
OUTPUT
File
PED_FILE
File
ZCALL_THRESHOLDS_FILE
String
ZCALL_VERSION
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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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description MergePedIntoVcf()
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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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ORIGINAL_VCF
@Argument(shortName="VCF", doc="The vcf containing the original autocall genotypes.") public File ORIGINAL_VCF
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PED_FILE
@Argument(shortName="PED", doc="PED file to be merged into VCF.") public File PED_FILE
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MAP_FILE
@Argument(shortName="MAP", doc="MAP file for the PED file.") public File MAP_FILE
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ZCALL_THRESHOLDS_FILE
@Argument(shortName="ZCALL_T_FILE", doc="The zcall thresholds file.") public File ZCALL_THRESHOLDS_FILE
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ZCALL_VERSION
@Argument(shortName="ZCALL_VERSION", doc="The version of zcall used") public String 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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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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