ProduceBeagleInput

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

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

Input

A VCF with variants to convert to Beagle format

Outputs

A single text file which can be fed to Beagle

Optional: A file with a list of markers

Examples

     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.

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).

CommandLineGATK

ProduceBeagleInput specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--variant	RodBinding[VariantContext]	NA	Input VCF file
Optional
--checkIsMaleOnChrX	boolean	false	Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.
--out	PrintStream	stdout	File to which BEAGLE input 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.

--checkIsMaleOnChrX / -checkIsMaleOnChrX ( boolean with default value false )

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.

--out / -o ( PrintStream with default value stdout )

File to which BEAGLE input should be written.

--variant / -V ( required RodBinding[VariantContext] )

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

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.