Package picard.vcf
Class VcfToIntervalList
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- picard.cmdline.CommandLineProgram
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- picard.vcf.VcfToIntervalList
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@DocumentedFeature public class VcfToIntervalList extends CommandLineProgram
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 Modifier and Type Class Description static class
VcfToIntervalList.VARIANT_ID_TYPES
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Field Summary
Fields Modifier and Type Field Description boolean
INCLUDE_FILTERED
static String
INCLUDE_FILTERED_SHORT_NAME
File
INPUT
static htsjdk.samtools.util.Log
LOG
File
OUTPUT
static VcfToIntervalList.VARIANT_ID_TYPES
VARIANT_ID_METHOD
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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 VcfToIntervalList()
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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.-
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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INCLUDE_FILTERED_SHORT_NAME
public static final String INCLUDE_FILTERED_SHORT_NAME
- See Also:
- Constant Field Values
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LOG
public static final htsjdk.samtools.util.Log LOG
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INPUT
@Argument(doc="The BCF or VCF input file. The file format is determined by file extension.", shortName="I") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="The output Picard Interval List.") public File 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
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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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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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