Collect statistics about sequence reads based on their SAM flags
java -jar GenomeAnalysisTK.jar -T FlagStat -R reference.fasta -I reads.bam [-o output.txt]
Argument name(s) | Default value | Summary | |
---|---|---|---|
Optional Outputs | |||
--out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists |