How to get list of variants after make_examples step? about deepvariant HOT 1 CLOSED

Hi @sophienguyen01
You can try https://github.com/google/deepvariant/blob/r1.6.1/deepvariant/labeler/labeled_examples_to_vcf.py
This is more experimental and not officially documented yet. But you can find in our Docker:
https://github.com/google/deepvariant/blob/r1.6.1/Dockerfile#L152

For now, please read the code and use the flags there. As mentioned, this is experimental and we have not officially supported it yet, so I can't say it'll work for the specific use case that you want. But you can at least look at the code and see whether you can adapt it.

Another more typical approach is to run through the rest of the steps (call_variants, postprocess_variants) and get the list of variants that way.

from deepvariant.