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  • BWA samse -n option

    I am having trouble with the -n option with bwa samse (version 0.5.3). If I either leave it off or use -n -1, I do get apparently good results in SAM format. But if I put any positive number in, I get something else. It looked like this for one case:
    >081017-and-081020:1:1:1715:1759 1 1
    PHIX174 -322 2

    Could anyone tell me what's going on here? I was expecting SAM output. How are we supposed to use this output?

    UPDATE:

    I looked again at the manual and this time I noticed the following:
    When -n is applied, multiple positions will be printed in a concise format. The ‘>’ line in the output shows the read name, the number of printed hits and the number of stored hits; the following lines give the chromosomal coordinates and the edit distance.

    So, that clears up what the output is. Basically, if I understand things, it is impossible to get multiple hit output in SAM format? Is this a limitation of SAM, or something else?
    Last edited by kellyv; 01-19-2010, 01:25 PM. Reason: noticed extra information partially answering question

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