@DocumentedFeature public final class VariantsToTable extends VariantWalker
This tool extracts specified fields for each variant in a VCF file to a tab-delimited table, which may be easier to work with than a VCF. By default, the tool only extracts PASS or . (unfiltered) variants in the VCF file. Filtered variants may be included in the output by adding the --show-filtered flag. The tool can extract both INFO (i.e. site-level) fields and FORMAT (i.e. sample-level) fields.
Use the `-F` argument to extract INFO fields; each field will occupy a single column in the output file. The field can be any standard VCF column (e.g. CHROM, ID, QUAL) or any annotation name in the INFO field (e.g. AC, AF). The tool also supports the following additional fields:
Use the `-GF` argument to extract FORMAT/sample-level fields. The tool will create a new column per sample with the name "SAMPLE_NAME.FORMAT_FIELD_NAME" e.g. NA12877.GQ, NA12878.GQ.
A tab-delimited file containing the values of the requested fields in the VCF file.
gatk VariantsToTable \
-V input.vcf \
-F CHROM -F POS -F TYPE -GF AD \
-O output.table
would produce a file that looks like:
CHROM POS TYPE HSCX1010N.AD HSCX1010T.AD
1 31782997 SNP 77,0 53,4
1 40125052 SNP 97,0 92,7
1 65068538 SNP 49,0 35,4
1 111146235 SNP 69,1 77,4
| Modifier and Type | Field and Description |
|---|---|
boolean |
errorIfMissingData
By default, this tool will write NA for missing data.
|
drivingVariantFileFEATURE_CACHE_LOOKAHEADaddOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAMEGATK_CONFIG_FILE, NIO_MAX_REOPENS, QUIET, specialArgumentsCollection, TMP_DIR, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
|---|
VariantsToTable() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(htsjdk.variant.variantcontext.VariantContext vc,
ReadsContext readsContext,
ReferenceContext ref,
FeatureContext featureContext)
Process an individual variant.
|
void |
onTraversalStart()
Operations performed just prior to the start of traversal.
|
getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartupgetBestAvailableSequenceDictionary, getProgressMeterRecordLabel, makeVariantFilter, requiresFeatures, traverseaddFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolkitShortName, getToolName, getTransformedReadStream, hasFeatures, hasIntervals, hasReads, hasReference, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalSuccess, requiresIntervals, requiresReads, requiresReference, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus@Advanced
@Argument(fullName="error-if-missing-data",
shortName="EMD",
doc="Fail on missing data",
optional=true)
public boolean errorIfMissingData
public void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(htsjdk.variant.variantcontext.VariantContext vc,
ReadsContext readsContext,
ReferenceContext ref,
FeatureContext featureContext)
VariantWalkerBaseapply in class VariantWalkerBasevc - 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).