Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample in input variant file.
These Read Filters are automatically applied to the data by the Engine before processing by VariantsToBeagleUnphased.
This tool applies the following downsampling settings by default.
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 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|
|NA||Input VCF file|
|stdout||File to which BEAGLE unphased genotypes should be written|
|0.0||Proportion of records to be used in bootstrap set|
|NA||Output a VCF with the records used for bootstrapping filtered out|
||?||String to identify missing data in beagle output|
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.
Proportion of records to be used in bootstrap set
double 0.0 [ [ -∞ ∞ ] ]
Output a VCF with the records used for bootstrapping filtered out
String to identify missing data in beagle output
File to which BEAGLE unphased genotypes should be written
Input VCF file
GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA