Lifts a VCF file over from one build to another.
These Read Filters are automatically applied to the data by the Engine before processing by LiftoverVariants.
This tool applies the following downsampling settings by default.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--variant||RodBinding[VariantContext]||NA||Input VCF file|
|--out||File||NA||File to which variants should be written|
|--newSequenceDictionary||File||NA||Sequence .dict file for the new build|
|--recordOriginalLocation||Boolean||false||Should we record what the original location was in the INFO field?|
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.
Sequence .dict file for the new build.
File to which variants should be written.
Should we record what the original location was in the INFO field?.
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 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.