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  • epigen
    replied
    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.

    Leave a comment:


  • dawe
    replied
    Originally posted by Protaeus View Post
    I have another BWA inquiry. How can one id the uniquely mapped reads from a sam/bam generated by BWA? Thanks for any thoughts.
    They have XT tag set to "U".

    Leave a comment:


  • Protaeus
    started a topic ID'ing Uniquely Mapped Regions in BWA

    ID'ing Uniquely Mapped Regions in BWA

    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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