Package picard.arrays
Class CombineGenotypingArrayVcfs
java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.CombineGenotypingArrayVcfs
A simple program to combine multiple genotyping array VCFs into one VCF
The input VCFs must have the same sequence dictionary and same list of variant loci.
The input files must not share sample Ids.
The input files must have the same contig lists.
Throws IllegalArgumentException if the contig lists
are not present in the input files, or are not identical
this class uses the GATK to merge headers, which may throw exceptions if the headers
cannot be merged. See VCFUtils.smartMergeHeaders for details.
An index file is created for the output file by default. Using an output file name with a
".gz" extension will create gzip-compressed output.
Note that this tool is written to handle a use case not supported by MergeVcfs (merging multiple
VCFs, each for a different sample).
Note also that this tool is similar intent to the GATK tool CombineVariants (which is in GATK3, but not in 4).
There are some array-specific features in this tool that probably could be generalized in CombineVariants when/if
that is installed in GATK4.
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Field Summary
FieldsFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
doWork()
Do the work after command line has been parsed.static htsjdk.variant.variantcontext.VariantContext
Merges multiple VariantContexts all for the same locus into a single hybrid.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 Details
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INPUT
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OUTPUT
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Constructor Details
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CombineGenotypingArrayVcfs
public CombineGenotypingArrayVcfs()
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Method Details
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doWork
public 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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merge
public static htsjdk.variant.variantcontext.VariantContext merge(List<htsjdk.variant.variantcontext.VariantContext> variantContexts) Merges multiple VariantContexts all for the same locus into a single hybrid.- Parameters:
variantContexts
- list of VCs- Returns:
- new VariantContext representing the merge of variantContexts
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