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Old 07-05-2011, 12:59 PM   #1
Protaeus
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Default BWA: Is alignment summary available?

Is there a tool associated with BWA that can provide a concise overall summary of the alignments/pairing, such as:
1. How many reads did not map?
2. How many single ends mapped?
3. How many reads were successfully paired
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Old 07-05-2011, 01:47 PM   #2
swbarnes2
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I don't think so. I use samtools flagstat.
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Old 07-05-2011, 06:12 PM   #3
DZhang
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I use picard
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