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  • guavajuice
    Junior Member
    • Mar 2010
    • 6
    #1

    bfast paired end flag

    I have a BFAST BAM with with version 0.6.3c

    When I do samtools view -f 0X0007 bam. I get back a list of paired end reads

    That means flags 0x0001, 0x0002, and 0x0004 are set. If the query is paired indicated by flag 01, and the pair is mapped (02),
    why is the query itself unmapped (04)? It seems contradictory to me.
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