Converts the input VCF into a format accepted by the Beagle imputation/analysis program.
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
These Read Filters are automatically applied to the data by the Engine before processing by ProduceBeagleInput.
This tool overrides the engine's default downsampling settings.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--variant||RodBinding[VariantContext]||NA||Input VCF file|
|--out||PrintStream||stdout||File to which BEAGLE input should be written|
|--checkIsMaleOnChrX||boolean||false||Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.|
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.
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.
File to which BEAGLE input should be written.
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 2.7-4-g46ca8c7 built at 2013/10/10 17:33:37.