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I have another BWA inquiry. How can one id the uniquely mapped reads from a sam/bam generated by BWA? Thanks for any thoughts.
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They have XT tag set to "U".Originally posted by Protaeus View Post -
You can use samtools view -q 1 to only output uniquely mapped reads (and omit both unmapped and ambiguous ones). Ambiguous reads that can be mapped to different locations with the same score have mapping quality 0 in BWA.Comment
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