Count the number of reads ending in insertions, deletions or soft-clips
java -jar GenomeAnalysisTK.jar -T CountTerminusEvent -R reference.fasta -I input.bam -o output.txt [-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 |