@DocumentedFeature public final class SelectVariants extends VariantWalker
This tool makes it possible to select a subset of variants based on various criteria in order to facilitate certain analyses. Examples of such analyses include comparing and contrasting cases vs. controls, extracting variant or non-variant loci that meet certain requirements, or troubleshooting some unexpected results, to name a few.
There are many different options for selecting subsets of variants from a larger callset:
There are also several options for recording the original values of certain annotations which are recalculated when one subsets the new callset, trims alleles, etc.
A variant call set in VCF format from which a subset can be selected.
A new VCF file containing the selected subset of variants.
*
gatk SelectVariants \
-R Homo_sapiens_assembly38.fasta \
-V input.vcf \
--select-type-to-include SNP \
-O output.vcf
gatk SelectVariants \
-R Homo_sapiens_assembly38.fasta \
-V gendb://genomicsDB \
-L 20 \
-O output.chr20.vcf
| Modifier and Type | Field and Description |
|---|---|
GATKPathSpecifier |
vcfOutput |
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, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
|---|
SelectVariants() |
| 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.
|
protected static boolean |
containsIndelLargerOrSmallerThan(htsjdk.variant.variantcontext.VariantContext vc,
int maxIndelSize,
int minIndelSize) |
protected CountingVariantFilter |
makeVariantFilter()
Create filters for variant types, ids, and genomic intervals.
|
void |
onTraversalStart()
Set up the VCF writer, the sample expressions and regexs, filters inputs, and the JEXL matcher
|
getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartup, traversegetBestAvailableSequenceDictionary, getDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, 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="Path to which variants should be written")
public GATKPathSpecifier vcfOutput
public void onTraversalStart()
onTraversalStart 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()
protected CountingVariantFilter makeVariantFilter()
makeVariantFilter in class VariantWalkerBaseprotected static boolean containsIndelLargerOrSmallerThan(htsjdk.variant.variantcontext.VariantContext vc,
int maxIndelSize,
int minIndelSize)