Hi GATK team,
I am posting this question for everyone's benefit as it will shed more light on how HaplotypeCaller and other GATK programs deal with low coverage positions.
For the sake of this example, let's assume we have a position no 1234 supported by 2 C reads, and let's also assume that there is enough evidence for the haplotype containing this read for it to be mapped to the reference, and let's also assume that we have set --minPruning to 1 so that this read does not get tossed out during re-alignment with HaplotypeCaller, and let's also assume that the reference is AC for this site, and let's assume we filter for annotations except for depth or coverage during VQSR, and let's finally assume that for some reason only 1 strand got sequenced at position 1234 during sequencing.
Questions:
1- Will the call at position 1234 likely be CC?
2- Will position 1234 likely not get called at all?
3- Will position 1234 get called as AC because that is what the reference has?