How to work with Deepvariant

Question

[vinaysbharadhwaj]

Hello, I am new to deep learning and I wanted to try out the Deep variant by google, but I got stuck while installing it. The guide given in the github is for google cloud but I wanted to try it out in my own system and the steps for doing so isn't given that clearly. I ran all the scripts and have basically installed tensorflow and bazel. But now I do not know how to train it and actually extract SNP's from it. Any help is highly appreciated, thank you

Link for Deepvariant - https://github.com/google/deepvariant/blob/r0.5/README.md

[GenoMax]

Tagging: arostami
mdepristo

Deep variant developers don't seem to participate here regularly. I have added deepvariant tag to this post which may send a ping to them.

[vinaysbharadhwaj]

Thank you so much, for some reason I wasn't able to add it myself. And as for the question, one person had asked in the github but the answer wasn't satisfactory, they said you can use the same method for Ubuntu 16 but I wasn't able to, so I asked here to know if anyone here has used it and has any tips for me

[GenoMax]

And you may indeed hear from someone. We have had only two past threads on this topic so far on Biostars.

[vinaysbharadhwaj]

Ok thank you so much

[Bioinformatics_NewComer]

I'd like to hear on this as well. Installation is a headache.

Answer 1

[alaincoletta]

Hi Vinay, we implemented the DeepVariant pipeline with Docker and Nextflow here

Lifebit integrate it the pipeline with example parameters

Would love your feedback on this.

Thanks!

[GenoMax]

The link you posted is just going to your company website. If you were specifically referring to a deepvariant pipeline then that is not serving the intended purpose. If you wish to advertise this tool then you could create a separate tool post rather than posting the same content in every thread tagged deepvariant.

[alaincoletta]

Sorry, I edited my reply and pointed to the pipeline source directly https://github.com/lifebit-ai/DeepVariant

Answer 2

[sangram_keshari]

Deepvariant on local system:

This is a link to nf-core pipeline to run on a local system with enough resources: https://github.com/nf-core/deepvariant