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Old 06-14-2011, 01:48 PM   #2
Location: Brock University

Join Date: Dec 2010
Posts: 66

BWA determines the suffix array intervals for each read during the 'aln' stage. If you're allowing errors (bwa aln -n #oferrors), a read can have many suffix array intervals of varying lengths.

The more (and larger) suffix array intervals a read has, the more work BWA has to go through during 'sampe' to pair it with its mate as there is a greater combinations of positions to consider for each mate... if the number of potential alignments exceeds the -o parameter (defaulted at 100 000), BWA just skips pairing altogether and leaves each mate aligned as if they were not mates at all in order to maintain an efficient alignment process.
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