Documentation

VariantsToVCF

Converts variants from other file formats to VCF format.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

Note that there must be a Tribble feature/codec for the file format as well as an adaptor.

Input

A variant file to filter.

Output

A VCF file.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T VariantsToVCF \
   -o output.vcf \
   --variant:RawHapMap input.hapmap \
   --dbsnp dbsnp.vcf
 

Additional Information

Read filters

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

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: -40 bp before the locus
  • Window stop: 40 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).

VariantsToVCF 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 variant file
Optional Inputs
--dbsnp
 -D
none dbSNP file
Optional Outputs
--out
 -o
stdout File to which variants should be written
Optional Parameters
--sample
NA The sample name represented by the variant rod

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.


--dbsnp / -D

dbSNP file

--dbsnp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

RodBinding[VariantContext]  none


--out / -o

File to which variants should be written

VariantContextWriter  stdout


--sample / -sample

The sample name represented by the variant rod
This argument is used for data (like GELI) with genotypes but no sample names encoded within.

String


--variant / -V

Input variant file
Variants from this input file are used by this tool as input.

--variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, OLDDBSNP, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

R RodBinding[Feature]


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA