Randomly split variants into different sets
This tool takes a VCF file, randomly splits variants into different sets, and writes the results to separate files. By default the tool splits the input into two new sets, but it can be made to output more than two separate call sets.
A variant call set to split.
The new callsets.
java -jar GenomeAnalysisTK.jar \ -T RandomlySplitVariants \ -R reference.fasta \ -V input.vcf \ -o1 output_1.vcf \ -o2 output_2.vcf
These Read Filters are automatically applied to the data by the Engine before processing by RandomlySplitVariants.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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).
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R RodBinding[VariantContext] NA
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.