read_GC.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_FILE, --input-file=INPUT_FILE | |
| Alignment file in BAM or SAM format. | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be called “uniquely mapped”. default=30 | |