java -jar GenomeAnalysisTK.jar -R reference.fasta -T CompareCallableLoci -comp1 callable_loci_1.bed -comp2 callable_loci_2.bed [-L input.intervals \] -o comparison.table
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Inputs | |||
| --comp1 | NA | First comparison track name | |
| --comp2 | NA | Second comparison track name | |
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --printstate  -printState | NA | If provided, prints sites satisfying this state pair | |