RandomlySplitVariants

Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview


Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by RandomlySplitVariants.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

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).

RandomlySplitVariants specific arguments

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
Required Inputs
--variant
 -V
NA Input VCF file
Optional Outputs
--out1
 -o1
stdout File #1 to which variants should be written
--out2
 -o2
NA File #2 to which variants should be written
Optional Parameters
--fractionToOut1
 -fraction
0.5 Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2
--numOfOutputVCFFiles
 -N
-1 number of output VCF files. Only works with SplitToMany = true
--prefixForAllOutputFileNames
 -baseOutputName
NA the name of the output VCF file will be: .split..vcf. Required with SplitToMany option
Optional Flags
--splitToManyFiles
 -splitToMany
false split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required

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.


--fractionToOut1 / -fraction

Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2

double  0.5  [ [ -?  ? ] ]


--numOfOutputVCFFiles / -N

number of output VCF files. Only works with SplitToMany = true

int  -1  [ [ 2  20 ]  ? ] ]


--out1 / -o1

File #1 to which variants should be written

VariantContextWriter  stdout


--out2 / -o2

File #2 to which variants should be written

File


--prefixForAllOutputFileNames / -baseOutputName

the name of the output VCF file will be: .split..vcf. Required with SplitToMany option

String


--splitToManyFiles / -splitToMany

split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required

boolean  false


--variant / -V

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

R RodBinding[VariantContext]


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA