LiftoverVariants

Lifts a VCF file over from one build to another.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

Note that the resulting VCF could be mis-sorted.

Additional Information

Read filters

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

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).

CommandLineGATK

LiftoverVariants specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--chain	File	NA	Chain file
--newSequenceDictionary	File	NA	Sequence .dict file for the new build
--variant	RodBinding[VariantContext]	NA	Input VCF file
Optional
--out	File	NA	File to which variants should be written
--recordOriginalLocation	Boolean	false	Should we record what the original location was in the INFO field?

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.

--chain / -chain ( required File )

Chain file.

--newSequenceDictionary / -dict ( required File )

Sequence .dict file for the new build.

--out / -o ( File )

File to which variants should be written.

--recordOriginalLocation / -recordOriginalLocation ( Boolean with default value false )

Should we record what the original location was in the INFO field?.

--variant / -V ( required RodBinding[VariantContext] )

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

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.