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Takes alleles from a variants file and breaks them up (if possible) into more basic/primitive alleles.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


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 will take an MNP (e.g. ACCCA -> TCCCG) and break it up into separate records for each component part (A-T and A->G). Note that this tool modifies only bi-allelic variants.


A variant set with any type of alleles.


A VCF with alleles broken into primitive types.


 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T VariantsToAllelicPrimitives \
   --variant input.vcf \
   -o output.vcf

Additional Information

Read filters

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

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

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).

--variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

R RodBinding[VariantContext]

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA