RandomlySplitVariants

Randomly split variants into different sets

Category Variant Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

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.

Input

A variant call set to split.

Output

The new callsets.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T RandomlySplitVariants \
   -R reference.fasta \
   -V input.vcf \
   -o1 output_1.vcf \
   -o2 output_2.vcf
 

Additional Information

Read filters

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


Command-line Arguments

Engine arguments

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.

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  NA


--prefixForAllOutputFileNames / -baseOutputName

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

String  NA


--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).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA


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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.