akolesnikov

Closing for inactivity. Please feel free to reopen if needed.

Hello @helizabeth1103, dv_constants.py is the part of DeepVariant installation. You may take a look at https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md#notes-on-singularity for more details on DeepVariant with Singularity. You may also check https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-training-case-study.md that shows...

Local realignment algorithm works as following: * Candidate windows across the genome are selected for reassembly by looking for any evidence of possible genetic variation, such as mismatching or soft...

Thank you for providing the reference. We were able to reproduce the issue locally. Meanwhile one workaround I'd like to suggest to analyze the specific position or small region where...

Looks like this is the GLnexus question. Could you please post the question at GLNexus [page ](https://github.com/dnanexus-rnd/GLnexus) Also, from the log output it looks like GLnexus was completed successfully.

Closing the issue. Feel free to reopen as needed.

Hi @kunmonster , Could you please provide a command line that you use to run DeepVariant?

Since sometimes warning messages from Tensorflow may be misleading. Could you please try running call_variants and at the same time monitor the GPU load to make sure the GPU is...

Did you run `tensorflow.test.is_gpu_available()` from the DeepVariant docker? Could you try the suggestion from this [thread](https://stackoverflow.com/questions/48658204/tensorflow-failed-call-to-cuinit-cuda-error-no-device)

Hi @MatthieuBeukers, Could you please include the exact command that you used to run your evaluations? In addition please specify the hardware specs.