|
--version |
show program’s version number and exit |
|
-h, --help |
show this help message and exit |
|
-b INPUT_BAM, --bam=INPUT_BAM |
| | Input BAM file. The BAM file should be sorted and
indexed using SAMtools
(http://samtools.sourceforge.net/). (mandatory) |
|
-c INPUT_CHIMERAS, --chimeras=INPUT_CHIMERAS |
| | Fusion file. This file can be 6 columns (chr1 start1
end1 chr2 start2 end2) or 8 columns (chr1 start1 end1
name1 chr2 start2 end2 name2) separated by Tab or
Space. Lines starting with ‘#’ will be ignored.
(mandatory) |
|
-o OUTPUT_FILE, --output=OUTPUT_FILE |
| | Prefix of output files. Four files will be created
including “prefix.fusion.sorted.bam”,
“prefix.fusion.bed”, “prefix.fusion.interact.bed” and
“prefix.fusion.summary.txt”. (mandatory) |
|
-q MAP_QUAL, --mapq=MAP_QUAL |
| | Mapping quality cutoff. default=30 |
|
-t, --track-header |
| | If set, add “track line” to the BED file. |
|
-k, --keep-unknown-mapq |
| | If set, keep alignments with unknown mapping quality
(i.e., MAPQ = 255). |