Is it possible to merge a Solid F3 and F5 bam into a paired end bam???
The paired end reads have been mapped seperated by bwa 0.5.9 and for a downstream analysis I need a bam that contains the paired reads.
Or redoing the mapping the only option?
BWA does support paired-end reads, which means that F3 and F5 are first mapped and then paired, but everything inside the same BWA run.
SOLiD's LifeScope has a "pairing" module inside its pipeline, which you could try calling individually by tweaking the conguration files, but since you're using BWA and not LifeScope I guess you are indeed trying to avoid Applied's software. as far as I know, there's no such stand-alone plugin out there that performs pairing only, so the best suggestion I can think of would be to remap those reads using both F3 and F5 information in the run definition, because building a custom script to parse both files looking for pairs would definitely take you much longer.
First you should not attempt to re-create a paired end mappings from single end mappings. Beside the complexity of the task you probably also won't be able to set the flags that depend on evaluating the best possible arrangement of the mate pair.
Since you will need to work in color space and bwa may not the best choice for that. I would evaluate other tools, although at this point I forgot what the options were since we have not needed to make use of such data.
I recall a post by Kevin on the Gattaca blog on mapping SOLiD reads with bwa:
http://kevin-gattaca.blogspot.com/2010/08/howto-do-bwa-mapping-in-colorspace.html
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version 2.3.6
Do you have more information on how to map the F3 and F5 reads as pairs using BWA? I thought that BWA (before fully dropping Solid at version 0.6.x ) doesn't have native support for Solid paired end , because the reverse read is not on the strand that BWA expects it to be.
I tried BWA quite a long time ago with SOLiD reads, since we have been focusing in LifeScope for a long time, so what I wrote above about it was just what I knew from the documentation. the best suggestion would be to contact directly Heng Li (user lh3 here, BWA's developer) and forward this question directly to him, as he's always very helpful.