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nickschurch 07-05-2013 07:37 AM

Switch strands of a bam file...
I have a bam file where the strand information has been unintentionally reversed. Is there an easy command in samtools for switching the strand information for every read? If not, what is the best way to do this? I guess I could loop though each read in python and switching the bit flag, but I really don't want to have to code this myself if there is a better (read faster) solution...

sdriscoll 07-05-2013 08:54 PM

I don't know of any standard tool that will do this. Code!

nickschurch 07-08-2013 07:21 AM

problem solved:

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