This question is specific to HaplotypeCaller. I know that this question is better asked at GATK forum. However, I didn't get a good answer. So I am hope to get a second opinion here.
I understand that, during germline calling, pairHMM calculates the likelihood of each haplotype by taking base quality into consideration. However, I didn't find any sort of minimum threshold of likelihood being set.
I suppose region with multiple mismatch gets low likelihood for all possible allele (say AA, AC and CC at given site). If no minimum threshold of likelihood being set, the allele with highest likelihood still get emitted? Or I missed something that prevent this from happening?