Package picard.fingerprint
Class CalculateFingerprintMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.fingerprint.CalculateFingerprintMetrics
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@DocumentedFeature public class CalculateFingerprintMetrics extends CommandLineProgram
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have. For example, if too many sites are heterozygous, that would get flagged.
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Field Summary
Fields Modifier and Type Field Description CrosscheckMetric.DataType
CALCULATE_BY
double
GENOTYPE_LOD_THRESHOLD
File
HAPLOTYPE_MAP
List<String>
INPUT
int
NUMBER_OF_SAMPLING
File
OUTPUT
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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 CalculateFingerprintMetrics()
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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.FingerprintMetrics
getFingerprintMetrics(Fingerprint fingerprint)
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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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INPUT
@Argument(shortName="I", doc="One or more input files (SAM/BAM/CRAM or VCF).") public List<String> INPUT
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OUTPUT
@Argument(shortName="O", doc="The output file to write (Metrics).") public File OUTPUT
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HAPLOTYPE_MAP
@Argument(shortName="H", doc="The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.") public File HAPLOTYPE_MAP
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CALCULATE_BY
@Argument(doc="Specificies which data-type should be used as the basic unit. Fingerprints from readgroups can be \"rolled-up\" to the LIBRARY, SAMPLE, or FILE level before being used. Fingerprints from VCF can be be examined by SAMPLE or FILE.") public CrosscheckMetric.DataType CALCULATE_BY
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GENOTYPE_LOD_THRESHOLD
@Argument(doc="LOD score threshold for considering a genotype to be definitive.") public final double GENOTYPE_LOD_THRESHOLD
- See Also:
- Constant Field Values
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NUMBER_OF_SAMPLING
@Argument(doc="Number of randomization trials for calculating the DISCRIMINATORY_POWER metric.") public final int NUMBER_OF_SAMPLING
- See Also:
- Constant Field Values
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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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getFingerprintMetrics
public FingerprintMetrics getFingerprintMetrics(Fingerprint fingerprint)
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