bwa sampe -c option

[cband]

Can anybody help me understand what the -c flag does for 'bwa sampe'? Information on this is pretty sparse and the source is pretty dense to figure this one out. Thanks a lot in advance!

bwa sampe

Options: -a INT   maximum insert size [500]
         -o INT   maximum occurrences for one end [100000]
         -n INT   maximum hits to output for paired reads [3]
         -N INT   maximum hits to output for discordant pairs [10]
         -c FLOAT prior of chimeric rate (lower bound) [1.0e-05]
         -f FILE  sam file to output results to [stdout]
         -r STR   read group header line such as `@RG\tID:foo\tSM:bar' [null]
         -P       preload index into memory (for base-space reads only)
         -s       disable Smith-Waterman for the unmapped mate
         -A       disable insert size estimate (force -s)

[joachim.jacob]

sampe -c

-c FLOAT prior of chimeric rate (lower bound) [1.0e-05]

I assume that this is the chance that a read is chimeric, i.e. composed of two unrelated parts of the genome. Default: at least 1 in 10000 reads is chimeric.