Package picard.arrays
Class CollectArraysVariantCallingMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.arrays.CollectArraysVariantCallingMetrics
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@DocumentedFeature public class CollectArraysVariantCallingMetrics extends CommandLineProgram
Collects summary and per-sample metrics about variant calls in a VCF file.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
static class
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
static class
CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
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Field Summary
Fields Modifier and Type Field Description static Double
CALL_RATE_PF_THRESHOLD
File
DBSNP
File
INPUT
int
NUM_PROCESSORS
File
OUTPUT
File
SEQUENCE_DICTIONARY
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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 CollectArraysVariantCallingMetrics()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.static boolean
getSexConcordance(String reportedSexString, String fingerprintSexString, String autocallSexString)
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Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, 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="Input vcf file for analysis") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="Path (except for the file extension) of output metrics files to write.") public File OUTPUT
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CALL_RATE_PF_THRESHOLD
@Argument(doc="The Call Rate Threshold for an autocall pass (if the observed call rate is > this value, the sample is considered to be passing)", optional=true) public static Double CALL_RATE_PF_THRESHOLD
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DBSNP
@Argument(doc="Reference dbSNP file in dbSNP or VCF format.") public File DBSNP
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SEQUENCE_DICTIONARY
@Argument(shortName="SD", optional=true, doc="If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.") public File SEQUENCE_DICTIONARY
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NUM_PROCESSORS
@Argument(doc="Split this task over multiple threads. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.") public int NUM_PROCESSORS
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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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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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