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Old 02-06-2012, 01:20 PM   #1
RockChalkJayhawk
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Location: Rochester, MN

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Default 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.
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Old 02-06-2012, 01:49 PM   #2
RockChalkJayhawk
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Eazy fix:

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