Package picard.vcf
Class SplitVcfs
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.SplitVcfs
Splits the input VCF file into two, one for indels and one for SNPs. The headers of the two output
files will be identical.
An index file is created for the output file by default. Using an output file name with a ".gz"
extension will create gzip-compressed output.
-
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
-
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
-
Field Details
-
INPUT
-
SNP_OUTPUT
@Argument(doc="The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.") public File SNP_OUTPUT -
INDEL_OUTPUT
@Argument(doc="The VCF or BCF file to which indel records should be written. The file format is determined by file extension.") public File INDEL_OUTPUT -
SEQUENCE_DICTIONARY
@Argument(shortName="D", doc="The index sequence dictionary to use instead of the sequence dictionaries in the input files", optional=true) public PicardHtsPath SEQUENCE_DICTIONARY -
STRICT
@Argument(doc="If true an exception will be thrown if an event type other than SNP or indel is encountered") public Boolean STRICT
-
-
Constructor Details
-
SplitVcfs
public SplitVcfs()
-
-
Method Details
-
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.
-