I am trying to figure out a way to split up a BAM file into many small pieces without splitting up read pairs. The resulting BAM files needs to be name-sorted, although that operation could be performed on each chunk after the splitting process.
As far as I can tell, there aren't any existing tools that do this. Does anyone know of anything?
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written
by
Ian Fiddes
1 answer
Since you have RNA-Seq in your keywords I assume this is RNA-Seq data. If so, if you split at intergenic regions you should de-couple a relatively small number of pairs. You would probably obtain a few thousand files. You can then use samtools fixmate to keep only paired reads within files.
In general, I think finding the optimal solution that minimises the number of decouplings is quite a difficult problem and it may be anyway impractical.
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It would be highly likely that name sorting it first and then splitting will be much much easier as pairs have the same name in a BAM file!
First thing that comes to my mind is that you could probably split over the centromere without issues, but I assume you want to split more than once.