java -jar GenomeAnalysisTK.jar -T SelectHeaders -R reference.fasta -V input.vcf -o output.vcf -hn FILTER -hn FORMAT -hn INFO
| 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 | |
| Optional Parameters | |||
| --exclude_header_name  -xl_hn | NA | Exclude header. Can be specified multiple times | |
| --header_expression  -he | NA | Regular expression to select many headers from the tracks provided. Can be specified multiple times | |
| --header_name  -hn | NA | Include header. Can be specified multiple times | |
| Optional Flags | |||
| --include_interval_names  -iln | false | If set the interval file name minus the file extension, or the command line intervals, will be added to the headers | |