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Old 12-09-2009, 06:02 AM   #1
aurelielaugraud
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Dear all,
Using bwa, I would like to select only reads that I am very sure about ...
it is to say, reads that have unique match (mismatch would be allowed as SNP are too frequent to consider the no-mismatch option, however, I am considering putting a limit but I don't really know which one, my reads are 75 bp illumina for the moment.)
I am trying to think to some solution regarding paired-ends : should both paired-ends be unique match, only one ? to be kept as very sure mapped reads.
I am not quite sure if I should play with bwa option to restrict the search or if I should use the sam format (I will probably need some help with the flag thing, it has been quite a while since I had a look at this) to select afterwards (if we consider that calculation time is not a problem ...) .
I would really appreciate comments, ideas and help

thanks a lot
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Old 12-09-2009, 06:27 AM   #2
lh3
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Set a cutoff on mapping quality. See also:

http://sourceforge.net/apps/mediawik...ing_quality.3F
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Old 12-09-2009, 06:31 AM   #3
aurelielaugraud
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thanks a lot
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Old 12-09-2009, 06:49 AM   #4
aurelielaugraud
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thanks lh3, where can I get some documentation about the mapping quality score (range, "stringentness" ...?
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