Andrew Carroll

Hi @jelber2 This is an interesting observation, thank you for bringing it up. So far, we've run DeepConsensus (trained on human) on several non-human species (multiple plants, frog and mouse)...

Hi @jelber2 I do see the email in my inbox when I search for your name. I am not sure how I missed itt originally. I will download the data...

Hi @jelber2 I was able to run DeepConsensus v0.3.1 on your data, and everything seems to have run smoothly. Although I don't have the empirical quality calculations relative to the...

Hi @gevro In terms of talking about model training possibilities by email, can you send a message to [email protected]. I can loop in Dan and we can continue discussion from...

Hi @SHuang-Broad By default, DeepVariant only looks at the content of the QUAL field (column 11) in order to populate the quality values. DeepVariant is able to look at and...

Hi @SHuang-Broad I would like to conduct some experiments myself to investigate whether this field might help. Unfortunately, with many things going on those experiments might take some time to...

Hi @Phillip-a-richmond Thank you for the report. You are correct, that the behavior out-of-the box for DeepTrio can currently be sub-optimal for the sex chromosomes in male samples. We've benchmarked...

Hi @Phillip-a-richmond As an additional follow-up, I am wondering if my answer is off the mark, that I have discussed this with respect of accuracy of calling, while you would...

Hi @Phillip-a-richmond I understand agree that this workflow is cumbersome and far from ideal. Here is the course of action that we'll propose to take: Within the next 2 weeks,...

Hi @Phillip-a-richmond Just as an update on this issue, we have the truth sets and have trained some experimental models. We're still in the process of refining these models, as...