3. Usage

Options:

--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).