java -jar GenomeAnalysisTK.jar -T RegenotypeVariants -R reference.fasta --variant input.vcf -o output.vcf
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --variant  -V | NA | Input VCF file | |
| Optional Outputs | |||
| --out  -o | stdout | File to which variants should be written | |