Package picard.arrays
Class GtcToVcf
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.arrays.GtcToVcf
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@DocumentedFeature public class GtcToVcf extends CommandLineProgram
Class to convert an Illumina GTC file into a VCF file.
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Field Summary
Fields Modifier and Type Field Description Integer
ANALYSIS_VERSION_NUMBER
File
CLUSTER_FILE
boolean
DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS
String
EXPECTED_GENDER
File
EXTENDED_ILLUMINA_MANIFEST
File
FINGERPRINT_GENOTYPES_VCF_FILE
File
GENDER_GTC
File
ILLUMINA_BEAD_POOL_MANIFEST_FILE
File
INPUT
File
OUTPUT
String
PIPELINE_VERSION
String
SAMPLE_ALIAS
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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 GtcToVcf()
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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 String
formatFloatForVcf(float value)
htsjdk.variant.variantcontext.Genotype
getGenotype(String sampleName, InfiniumGTCRecord infiniumGtcRecord, IlluminaManifestRecord record, htsjdk.variant.variantcontext.Allele A, htsjdk.variant.variantcontext.Allele B)
protected boolean
requiresReference()
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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, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="GTC file to be converted") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="The output VCF file to write.") public File OUTPUT
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EXTENDED_ILLUMINA_MANIFEST
@Argument(shortName="MANIFEST", doc="An Extended Illumina Manifest file (csv). This is an extended version of the Illumina manifest it contains additional reference-specific fields") public File EXTENDED_ILLUMINA_MANIFEST
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CLUSTER_FILE
@Argument(shortName="CF", doc="An Illumina cluster file (egt)") public File CLUSTER_FILE
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ILLUMINA_BEAD_POOL_MANIFEST_FILE
@Argument(shortName="BPM_FILE", doc="The Illumina Bead Pool Manifest (.bpm) file") public File ILLUMINA_BEAD_POOL_MANIFEST_FILE
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EXPECTED_GENDER
@Argument(shortName="E_GENDER", doc="The expected gender for this sample.", optional=true) public String EXPECTED_GENDER
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SAMPLE_ALIAS
@Argument(doc="The sample alias") public String SAMPLE_ALIAS
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PIPELINE_VERSION
@Argument(doc="The version of the pipeline used to generate this VCF", optional=true) public String PIPELINE_VERSION
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ANALYSIS_VERSION_NUMBER
@Argument(doc="The analysis version of the data used to generate this VCF", optional=true) public Integer ANALYSIS_VERSION_NUMBER
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GENDER_GTC
@Argument(shortName="G_GTC", doc="An optional GTC file that was generated by calling the chip using a cluster file designed to optimize gender calling.", optional=true) public File GENDER_GTC
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FINGERPRINT_GENOTYPES_VCF_FILE
@Argument(shortName="FP_VCF", doc="The fingerprint VCF for this sample", optional=true) public File FINGERPRINT_GENOTYPES_VCF_FILE
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DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS
@Argument(doc="Causes the program to fail if it finds a case where there is a call on an assay that is flagged as \'zeroed-out\' in the Illumina cluster file.", optional=true) public boolean DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS
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Method Detail
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requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
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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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getGenotype
public htsjdk.variant.variantcontext.Genotype getGenotype(String sampleName, InfiniumGTCRecord infiniumGtcRecord, IlluminaManifestRecord record, htsjdk.variant.variantcontext.Allele A, htsjdk.variant.variantcontext.Allele B)
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formatFloatForVcf
public static String formatFloatForVcf(float value)
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