Converts the input VCF into a format accepted by the Beagle imputation/analysis program.

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS



A VCF with variants to convert to Beagle format


A single text file which can be fed to Beagle

Optional: A file with a list of markers


     java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
      -R reffile.fasta -T ProduceBeagleInput \
      -V path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output

Additional Information

Read filters

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

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).

ProduceBeagleInput 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 BEAGLE input should be written
Optional Flags
false Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.

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.

--checkIsMaleOnChrX / -checkIsMaleOnChrX

Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.
If sample gender is known, this flag should be set to true to ensure that Beagle treats male Chr X properly.

boolean  false

--out / -o

File to which BEAGLE input should be written

PrintStream  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 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA