Converts variants from other file formats to VCF format.
Note that there must be a Tribble feature/codec for the file format as well as an adaptor.
A variant file to filter.
A VCF file.
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T VariantsToVCF \ -o output.vcf \ --variant:RawHapMap input.hapmap \ --dbsnp dbsnp.vcf
These Read Filters are automatically applied to the data by the Engine before processing by VariantsToVCF.
This tool uses a sliding window on the reference.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--variant||RodBinding[Feature]||NA||Input variant file|
|--out||VariantContextWriter||stdout||File to which variants should be written|
|--sample||String||NA||The sample name represented by the variant rod|
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.
File to which variants should be written.
The sample name represented by the variant rod. This argument is used for data (like GELI) with genotypes but no sample names encoded within.
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.