Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.
These Read Filters are automatically applied to the data by the Engine before processing by RandomlySplitVariants.
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 #1 to which variants should be written|
|NA||File #2 to which variants should be written|
|0.5||Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2|
|-1||number of output VCF files. Only works with SplitToMany = true|
|NA||the name of the output VCF file will be:
|false||split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required|
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.
Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2
double 0.5 [ [ -? ? ] ]
number of output VCF files. Only works with SplitToMany = true
int -1 [ [ 2 20 ] ? ] ]
File #1 to which variants should be written
File #2 to which variants should be written
the name of the output VCF file will be:
split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required
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).
GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA