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Old 08-19-2009, 12:28 PM   #1
baohua100
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Location: Canada

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Default MAQ paired-end alignment parameters

maq map aln.map ref.bfa 1.bfq 2.bfq -a 500

-a INT max distance between two paired reads [250]

when I use -a 500 the alignmnet output also contains the pairs whose distance is larger than 500.

maq pileup
-p discard abnormal pairs

what's the standard MAQ consinder which pairs are abnormal pairs?
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