fe0b5e0fbe
When a sample has multiple spanning deletions and we are asked to assign likelihoods to the spanning deletion allele, we currently choose the first deletion. Valentin pointed out that this isn't desired behavior. I promised Valentin that I would address this issue, so here it is. I do not believe that the correct thing to do is to sum the likelihoods over all spanning deletions (I came up with problematic cases where this breaks down). So instead I'm using a simple heuristic approach: using the hom alt PLs, find the most likely spanning deletion for this position and use its likelihoods. In the 10K-sample VCF from Monkol there were only 2 cases that this problem popped up. In both cases the heuristic approach works well. |
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