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Specify the correct sample name for empty VCFs instead of `default`

See original GitHub issue

Describe the issue: DeepVariant currently outputs default as the sample name for empty VCFs (related to the fix in #186 ). Ideally, the sample_name should be transferred from the original BAM file, but if that is too difficult to implement (since there are no examples), I think it would also be ok if we let the user customize this ID. One suggestion is that it can use the value provided by the --sample_name flag (currently, used for make_examples, but I think it can also be reused for postprocess_variants).

Using default causes issues in pipelines where the VCF is used downstream of DeepVariant (e.g. merging the VCF with other callers; or even within DeepVariant in a pipeline that scatters calling across multiple chromosomes and tries to gather them and some of those VCFs are empty).

Setup

DeepVariant version: v0.10.0
Installation method (Docker, built from source, etc.): docker

Issue Analytics

State:
Created 3 years ago
Comments:5 (2 by maintainers)

Top GitHub Comments

1reaction

gunjanbaidcommented, Aug 19, 2020

The functionality has been implemented in the internal codebase and will be available in the next release.

1reaction

pichuancommented, Aug 14, 2020

Thanks for the suggestion @arostamianfar . Sounds like a good suggestion and should be easy to do : adding a flag to postprocess_variants. If sample_name is specified for run_deepvariant.py, we’ll use it for both.

I’ll file an internal issue to track this, and we should be able to have this in our next release.

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