java -jar GenomeAnalysisTK.jar -T QualifyMissingIntervals -R reference.fasta -I input.bam -o output.grp -L input.intervals -cds cds.intervals -targets targets.intervals
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Parameters | |||
| --targetsfile  -targets | NA | Undocumented option | |
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --baitsfile  -baits | NA | Undocumented option | |
| --coveragethreshold  -cov | 20 | minimum coverage to be considered sequenceable | |
| --gcthreshold  -gc | 0.3 | upper and lower bound for an interval to be considered high/low GC content | |
| --intervalsizethreshold  -size | 10 | minimum interval length to be considered | |
| --mappingthreshold  -mmq | 20 | minimum mapping quality for it to be considered usable | |
| --qualthreshold  -mbq | 20 | minimum base quality for it to be considered usable | |