Package picard.arrays
Class CombineGenotypingArrayVcfs
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.arrays.CombineGenotypingArrayVcfs
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@DocumentedFeature public class CombineGenotypingArrayVcfs extends CommandLineProgram
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
Fields Modifier and Type Field Description List<File>
INPUT
File
OUTPUT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, 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 Constructor Description CombineGenotypingArrayVcfs()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
doWork()
Do the work after command line has been parsed.static htsjdk.variant.variantcontext.VariantContext
merge(List<htsjdk.variant.variantcontext.VariantContext> variantContexts)
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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Method Detail
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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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