base counts per position

[jpdna]

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.
The returned data would be a tuple of such counts for each position in the reference genome.

This exact functionality is now provided in this tool:
https://github.com/genome/bam-readcount
but is slow.

@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:

1. naive / exploratory variant calling where you want just these counts to explore what sort of test to do

• especially in the context of somatic calling where you are want to interpret only a 5-10% variant allele fraction

2. evaluate the background noise/bias at positions

[fnothaft]

Hi @jpdna! In avocado, I've just got the logic for a more restricted case: ref vs. alt. That said, it wouldn't be arduous to add. Do you mind opening said issue against Avocado?

[fnothaft]

Moved downstream to bigdatagenomics/avocado#297.