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