Convert variants from other file formats to VCF format
Note that there must be a Tribble feature/codec available for the file format as well as an adaptor.
A variant file to convert.
A VCF file.
java -jar GenomeAnalysisTK.jar \ -T VariantsToVCF \ -R reference.fasta \ -o output.vcf \ --variant:RawHapMap input.hapmap
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.
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.
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|
|NA||Input variant file|
|stdout||File to which variants should be written|
||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.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
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.
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
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.