Package picard.vcf
Class VcfToIntervalList
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.VcfToIntervalList
Converts a VCF or BCF file to a Picard Interval List.
This tool creates a Picard Interval List from a VCF or BCF. It is important that the file extension is included as the file format is determined by the file extension. Variants that were filtered can be included in the output interval list by setting INCLUDE_FILTERED to true.
Inputs
- A BCF or VCF input file
- Boolean if variants that were filtered should be included in the output interval list
Output
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A Picard Interval List
Usage example:
java -jar picard.jar VcfToIntervalList \ I=input_variants.vcf \ O=output.interval_list
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionboolean
static final String
static final htsjdk.samtools.util.Log
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 -
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
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Field Details
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INCLUDE_FILTERED_SHORT_NAME
- See Also:
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LOG
public static final htsjdk.samtools.util.Log LOG -
INPUT
@Argument(doc="The BCF or VCF input file. The file format is determined by file extension.", shortName="I") public File INPUT -
OUTPUT
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VARIANT_ID_METHOD
@Argument(doc="Controls the naming of the resulting intervals. When set to CONCAT_ALL (the default), each resulting interval will be named the concatenation of the variant ID fields (if present), or \'interval-<number>\' (if not) with a pipe \'|\' separator. If set to USE_FIRST, only the first name will be used.") public static VcfToIntervalList.VARIANT_ID_TYPES VARIANT_ID_METHOD -
INCLUDE_FILTERED
@Argument(shortName="IF", doc="Include variants that were filtered in the output interval list.", optional=true) public boolean INCLUDE_FILTERED
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Constructor Details
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VcfToIntervalList
public VcfToIntervalList()
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Method Details
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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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