@DocumentedFeature public final class UpdateVCFSequenceDictionary extends VariantWalker
This tool is designed to update the sequence dictionary in a variant file using a dictionary from another variant, alignment, dictionary, or reference file. The dictionary must be valid, i.e. must contain a sequence record, for all variants in the target file. The dictionary lines start with '##contig='.
By specifying both --replace and --disable-sequence-dictionary-validation, one can force replace an invalid sequence dictionary in a variant file with a valid sequence dictionary in another file.
gatk UpdateVCFSequenceDictionary \
-V cohort.vcf.gz \
--source-dictionary sample.bam \
--output cohort_replacedcontiglines.vcf.gz \
--replace=true
gatk UpdateVCFSequenceDictionary \
-V resource.vcf.gz \
--source-dictionary reference.dict \
--output resource_newcontiglines.vcf.gz
gatk UpdateVCFSequenceDictionary \
-V resource.vcf.gz \
-R reference.fasta \
--output resource_newcontiglines.vcf.gz
The -O argument specifies the name of the updated file. The --source-dictionary argument specifies the input sequence dictionary. The --replace argument is optional, and forces the replacement of the dictionary if the input file already has a dictionary.
| Modifier and Type | Field and Description |
|---|---|
static java.lang.String |
DICTIONARY_ARGUMENT_NAME |
java.lang.String |
outFile |
static java.lang.String |
REPLACE_ARGUMENT_NAME |
drivingVariantFileDEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES, genomicsDBOptionsaddOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArgumentsGATK_CONFIG_FILE, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
|---|
UpdateVCFSequenceDictionary() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(htsjdk.variant.variantcontext.VariantContext vc,
ReadsContext readsContext,
ReferenceContext ref,
FeatureContext featureContext)
Process an individual variant.
|
void |
closeTool()
Close out the new variants file.
|
htsjdk.samtools.SAMSequenceDictionary |
getBestAvailableSequenceDictionary()
Overriding the superclass method to preferentially
choose the sequence dictionary from the driving source of variants.
|
void |
onTraversalStart()
Operations performed just prior to the start of traversal.
|
getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartup, traversegetDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, makeVariantFilter, requiresFeaturesdirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalSuccess, requiresIntervals, requiresReads, requiresReference, transformTraversalIntervals, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus@Argument(fullName="output",
shortName="O",
doc="File to which updated variants should be written")
public java.lang.String outFile
public static final java.lang.String DICTIONARY_ARGUMENT_NAME
public static final java.lang.String REPLACE_ARGUMENT_NAME
public void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(htsjdk.variant.variantcontext.VariantContext vc,
ReadsContext readsContext,
ReferenceContext ref,
FeatureContext featureContext)
VariantWalkerapply in class VariantWalkervc - Current variant being processed.readsContext - Reads overlapping the current variant. Will be an empty, but non-null, context object
if there is no backing source of reads data (in which case all queries on it will return
an empty array/iterator)ref - Reference bases spanning the current variant. Will be an empty, but non-null, context object
if there is no backing source of reference data (in which case all queries on it will return
an empty array/iterator). Can request extra bases of context around the current variant's interval
by invoking ReferenceContext.setWindow(int, int)
on this object before calling ReferenceContext.getBases()featureContext - Features spanning the current variant. Will be an empty, but non-null, context object
if there is no backing source of Feature data (in which case all queries on it will return an
empty List).public void closeTool()
public htsjdk.samtools.SAMSequenceDictionary getBestAvailableSequenceDictionary()
VariantWalkerBasegetBestAvailableSequenceDictionary in class VariantWalkerBasenull if no one dictionary is the best one.