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.

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).

CommandLineGATK

VariantsToVCF 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
--variant	RodBinding[Feature]	NA	Input variant file
Optional
--dbsnp	RodBinding[VariantContext]	none	dbSNP file
--out	VariantContextWriter	stdout	File to which variants should be written
--sample	String	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 ( RodBinding[VariantContext] with default value none )

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

--out / -o ( VariantContextWriter with default value stdout )

File to which variants should be written.

--sample / -sample ( String )

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

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

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

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