Switch strands of a bam file...

nickschurch · 07-05-2013, 08:37 AM

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, 09:54 PM

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

nickschurch · 07-08-2013, 08:21 AM

problem solved:

https://pypi.python.org/pypi?name=ng...action=display

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07-05-2013, 08:37 AM	#1
nickschurch Junior Member Location: Aberdeen Join Date: Jul 2012 Posts: 6	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...

07-05-2013, 09:54 PM	#2
sdriscoll I like code Location: San Diego, CA, USA Join Date: Sep 2009 Posts: 438	I don't know of any standard tool that will do this. Code! __________________ /* Shawn Driscoll, Gene Expression Laboratory, Pfaff Salk Institute for Biological Studies, La Jolla, CA, USA */

07-08-2013, 08:21 AM	#3
nickschurch Junior Member Location: Aberdeen Join Date: Jul 2012 Posts: 6	problem solved: https://pypi.python.org/pypi?name=ng...action=display