java -jar GenomeAnalysisTK.jar -T Pileup -R reference.fasta -I my_reads.bam -L chr1:257-267 -o output.txt
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Inputs | |||
| --metadata | [] | ROD file containing metadata | |
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Flags | |||
| --showVerbose  -verbose | false | Add an extra verbose section to the pileup output | |