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Old 08-28-2013, 01:10 AM   #1
Pengfei Liu
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Location: Beijing

Join Date: Nov 2012
Posts: 16
Post how many mismatches does BWA-MEM tolerate during mapping

Hi,
Recently I am trying to use BWA-MEM to do alignment on PE-90 reads, I have some questiones list as following;


1,how many mismatches does BWA-MEM tolerate during mapping?
Does the following still applied to BWA-MEM:
‘Given a read of length m, BWA only tolerates a hit with at most k differences
(mismatches or gaps), where k is chosen such that <4% of m-long reads with
2% uniform base error rate may contain differences more thank. With this
configuration, for 15–37 bp reads,kequals 2; for 38–63 bp,k=3; for 64–92
bp,k=4; for 93–123 bp,k=5; and for 124–156 bp reads,k=6.’(Li and Durbin, 2009)

2,In bwa-aln sampe,the mismatch number could be setted by the ‘-n’option。
By default,what is the number of mismatch setted and how to set it in BWA-MEM?

3, Mapping quality is assigned for individual read, not for a read pair.so if I use '-q 30' to extract PE reads, some of the reads will lose their mate-pair, am I right? Are there any ideas on how to extract pair-reads (reads and its mate) with '-q 30' for both of them?

I have read the manual and the BWA-MEM paper, but sitll didn't get answers.

Any suggestions are appreciated!

Pengfei Liu
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