I had an issue related to this a while back but don't see it, so here again:
It would be really useful to be able to query an alignment file (BAM/ADAM) to count the number of bases (A/C/G/T, insert / delete) at each base in the genome.
This exact functionality is now provided in this tool:
@fnothaft - I'm sure this sort of functionality exists as a step in Avocado, can you point me where to look?
The applications I have for this are:
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