Showing docs for version 3.7-0

VariantsToVCF

Convert variants from other file formats to VCF format

Category Variant Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

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

Input

A variant file to convert.

Output

A VCF file.

Usage example

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

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

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

CommandLineGATK

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

This argument supports reference-ordered data (ROD) files in the following formats: 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 NA

--variant / -V

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

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

R RodBinding[Feature] NA