I have an indexed BAM file containing long-read sequencing data and I'd like to split the reads contained within into those with a known deletion and those without the deletion (I have the deletion coordinates available to me) when mapped against the hg38 genome. Ideally I'd like to end up with two BAM files (one with reads containing the deletion and one without) for downstream analysis. I've searched a bit online and haven't really found any tools that do exactly that, but this seems like a common enough task that there has to be something.
Thanks in advance for any help/guidance!
In addition to @gringer's great answer, I decided to write a small python script myself that solves my issue using pysam, the fruits of which can be found here. If anyone has any feedback or suggestions on it I'll happily take them, as I'm still very new to this. It's undergone very little testing, so user be warned.