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Old 08-24-2011, 12:36 PM   #1
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Location: State College, PA

Join Date: Jul 2009
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Default how to filter BWA paired-end alignments?


I want to filter my BAM alignments (generated using BWA on paired-end Illumina reads) to retain only those read pairs where at least one of the reads of the pair has unique mapping. Is there a way of doing this using the tag information available in the SAM file? or does anyone know of a tool that does something on these lines? Any suggestion will be greatly appreciated.

Thanks in advance..
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