cmuts gen

CLI Options

Output

Option	Description
-o, --output PREFIX	write PREFIX.bam and PREFIX.fasta (required)
--format FORMAT	alignment format to write (bam, sam; default bam)

Layout

Option	Description
--references N	how many references to write (default 100)
--ref-length DISTRIBUTION	length of each reference (default 400)
--covered F	fraction of references receiving any reads (0 to 1; default 1)
--reads-per-ref DISTRIBUTION	reads on each covered reference (default 20)

Reads

Option	Description
--read-length DISTRIBUTION	reference span each read covers (default 100:400)
--mapq DISTRIBUTION	mapping quality of each read (default 0,1,10,30,42,60)
--base-quality DISTRIBUTION	PHRED score of each base (default 30:40)
--reverse F	fraction of reads on the reverse strand (0 to 1; default 0.5)
--unmapped DISTRIBUTION	reads aligning nowhere (default 10)

Differences from the reference

Option	Description
--mismatch-rate F	per aligned base (0 to 1; default 0.01)
--insertions DISTRIBUTION	insertion events per read (default 0:1)
--insertion-length DISTRIBUTION	bases per insertion (default 1:5)
--deletions DISTRIBUTION	deletion events per read (default 0:1)
--deletion-length DISTRIBUTION	bases per deletion (default 1:3)
--soft-clips DISTRIBUTION	clipped ends per read, none through both (default 0:2)
--soft-clip-length DISTRIBUTION	bases per clipped end (default 5:30)

Determinism

Option	Description
--seed N	everything generated follows from this (default 1)

Information

Option	Description
-h, --help	show this help and exit
-V, --version	show the version and exit

Advanced

Accepted, and left out of --help.

Option	Description
--dump-options	describe every argument as JSON and exit