FilterLiftedVariants

Filters a lifted-over VCF file for ref bases that have been changed.

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. FilteredLiftedVariants is intended to be the second of two processing steps for the liftover process. The first step is to run LiftoverVariants on your VCF file. 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.

Additional Information

Read filters

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

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Window size

This tool uses a sliding window on the reference.

  • Window start: 0 bp before the locus
  • Window stop: 100 bp after the locus

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).

FilterLiftedVariants 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).

--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