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
but I think it is interpreting as -F 1036 (which is not what I want). Is there any way around this?
Thanks in advance.
I tried
Code:
samtools view -F 8 -F 4 -F 1024 $BAM
Thanks in advance.
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