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  • Find mates in a SAM file

    I want to identify the actual pairs of reads in a SAM file that potentially has multiple alignments for the same given pair.

    Is it sufficient to check whether two lines in the SAM file have same QNAME?

    Do I have to check for POS (start) and PNEXT (start of mate) fields and make sure they are matching between two lines?

    I am aware of the meaning of SAM flags to identify paired and mapped reads. Simply checking the flag, however, does not allow me to identify the actual pair.

    Thanks in advance.

  • #2
    cross-posted: https://www.biostars.org/p/149205/

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