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Simplify multi-nucleotide variants (MNPs) into more basic/primitive alleles.

Category Variant Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


This tool will take an MNP (e.g. ACCCA -> TCCCG) and break it up into separate records for each component part (A-T and A->G).


A variant set with any type of alleles.


A VCF with alleles broken into primitive types.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T VariantsToAllelicPrimitives \
   -R reference.fasta \
   -V input.vcf \
   -o output.vcf


  • For now this tool modifies only multi-nucleotide polymorphisms (MNPs) and leaves SNPs, indels, and complex substitutions as is, although one day it may be extended to handle the complex substitution case.
  • This tool modifies only bi-allelic variants.

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by VariantsToAllelicPrimitives.

Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

VariantsToAllelicPrimitives specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Inputs
NA Input VCF file
Optional Outputs
stdout File to which variants should be written

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--out / -o

File to which variants should be written

VariantContextWriter  stdout

--variant / -V

Input VCF file
Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.