java -jar GenomeAnalysisTK.jar -T CountIntervals -R reference.fasta -o output.txt -check intervals.list
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Inputs | |||
| --check | [] | Any number of RODs | |
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --numOverlaps  -no | 2 | Count all occurrences of X or more overlapping intervals; defaults to 2 | |