Documentation

LiftoverVariants

Lifts a VCF file over from one build to another.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

"Lifting over" variants means adjusting variant calls from one reference to another. Specifically, the process adjusts the position of the call to match the corresponding position on the target reference. For example, if you have variants called from reads aligned to the hg19 reference, and you want to compare them to calls made based on the b37 reference, you need to liftover one of the callsets to the other reference. LiftoverVariants is intended to be the first of two processing steps for the liftover process. The second step is to run FilterLiftedVariants on the output of LiftoverVariants. This will produce valid well-behaved VCF files, where you'll see that the contig names in the header have all been correctly replaced. To be clear, the VCF resulting from the LiftoverVariants run is not guaranteed to be valid according to the official specification. The file could possibly be mis-sorted and the header may not be complete. That is why you need to run FilterLiftedVariants on it.

Additional Information

Read filters

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

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).

LiftoverVariants 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
Required Outputs
--out
 -o
NA File to which variants should be written
Required Parameters
--chain
NA Chain file
--newSequenceDictionary
 -dict
NA Sequence .dict file for the new build
Optional Flags
--recordOriginalLocation
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

Chain file

R File


--newSequenceDictionary / -dict

Sequence .dict file for the new build

R File


--out / -o

File to which variants should be written

R File


--recordOriginalLocation / -recordOriginalLocation

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

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 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA