java -jar GenomeAnalysisTK.jar -T FastaReferenceMaker -R reference.fasta -o output.fasta -L input.intervals
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --lineWidth  -lw | 60 | Maximum length of sequence to write per line | |
| Optional Flags | |||
| --rawOnelineSeq  -raw | false | Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity) | |