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Old 07-02-2015, 08:36 AM   #1
PFS
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Default 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.
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Old 07-02-2015, 09:57 AM   #2
lindenb
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cross-posted: https://www.biostars.org/p/149205/
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