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  • RockChalkJayhawk
    Senior Member
    • Mar 2009
    • 192

    #1

    BAM flags using "OR"

    I'm trying to extract all reads where both are mapped (but not necessarily in the proper orientation/size) and remove PCR duplicates.
    I tried
    Code:
    samtools view  -F 8 -F 4 -F 1024 $BAM
    but I think it is interpreting as -F 1036 (which is not what I want). Is there any way around this?

    Thanks in advance.
  • RockChalkJayhawk
    Senior Member
    • Mar 2009
    • 192

    #2
    Eazy fix:

    Code:
    samtools view  -h -f1 -F 4 $BAM|samtools view -S  -F 8 -|samtools view -S -F  1024

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