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Old 10-28-2010, 04:40 AM   #2
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Join Date: Oct 2008
Posts: 323

Study carefully the SAM specification, particularly the flag field. Once you know
what flag to use, go ahead and use the filter capabilities in samtools view (-f/-F INT)
to extract the reads you are interested on.

For example (show me reads where the mate is ummapped):
$  samtools view -f 8 foo.bam
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