UPdated model for RNA-seq variant analysis using Deepvariant 1.9.0

[Antonio-GiTu]

Hello, a pleasure to meet you.

We are interested in performing variant calling from RNA-seq data. We are currently using the 1.9.0 version of Deepvariant and we would like to keep doing it. Looking thought the repository, we came across the following case study: https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-rnaseq-case-study.md, but it seems that the model used dates back to the 1.4.0 version. When looking for an updated model, we ended up here: https://42basepairs.com/browse/gs/deepvariant/models/DeepVariant, and we realized that the only RNA-seq model available is the one from the 1.4 version. The changelog seems to confirm this.

Our question would be if there is an updated RNA-seq model for the last Deepvariant version available, and in the case there is not, is there a way to maybe train or obtain one ourselves?

Thank you so much in advance. If more info or context is needed I'll be more than happy to provide.

[danielecook]

@Antonio-GiTu we are actively working on updating the RNA-seq model for our next version. As soon as it is available I will provide an update.

If you are interested in training a model yourself, you can follow the training tutorial