@DocumentedFeature public class VcfToIntervalList extends CommandLineProgram
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.
java -jar picard.jar VcfToIntervalList \
I=input_variants.vcf \
O=output.interval_list
| Modifier and Type | Field | Description |
|---|---|---|
boolean |
INCLUDE_FILTERED |
|
static String |
INCLUDE_FILTERED_SHORT_NAME |
|
File |
INPUT |
|
static htsjdk.samtools.util.Log |
LOG |
|
File |
OUTPUT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
VcfToIntervalList() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParserpublic static final String INCLUDE_FILTERED_SHORT_NAME
public static final htsjdk.samtools.util.Log LOG
@Argument(doc="The BCF or VCF input file. The file format is determined by file extension.",
shortName="I")
public File INPUT
@Argument(shortName="O",
doc="The output Picard Interval List.")
public File OUTPUT
@Argument(shortName="IF",
doc="Include variants that were filtered in the output interval list.",
optional=true)
public boolean INCLUDE_FILTERED
public static void main(String[] argv)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram