RegenotypeVariants

Regenotypes the variants from a VCF containing PLs or GLs.

Category Variant Discovery Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

This tool triggers re-genotyping of the samples through the Exact Allele Frequency calculation model. Note that this is truly the mathematically correct way to select samples from a larger set (especially when calls were generated from low coverage sequencing data); using the hard genotypes to select (i.e. the default mode of SelectVariants) can lead to false positives when errors are confused for variants in the original genotyping. This functionality used to comprise the --regenotype option in SelectVariants but we pulled it out into its own tool for technical purposes.

Input

A variant set to regenotype.

Output

A re-genotyped VCF.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T RegenotypeVariants \
   -R reference.fasta \
   --variant input.vcf \
   -o output.vcf
 

Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using this option.


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.

RegenotypeVariants 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
--out
 -o
stdout File to which variants should be written

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.


--out / -o

File to which variants should be written

VariantContextWriter  stdout


--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.