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  • bwa sampe -c option

    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!

    Code:
    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)

  • #2
    sampe -c

    Code:
    -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.
    www.bits.vib.be

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