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I believe `sites` and `variants` should be equivalent. I see that there is a warning emitted by GATK4 at sites that are not het, but it shouldn't be an error. If you're getting an error can you please…
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Implement whatever model comes out of #3087.
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Hi, I followed and successfully ran the [google cloud tutorial](https://cloud.google.com/genomics/docs/tutorials/gatk). But when I tried to run the [data processing workflow](https://github.com/gatk-w…
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I'm looking into migrating custom GATK3 variant Info/GenotypeAnnotations to GATK4. The annotate() method in GATK3 was passed a sizable amount of context. This is greatly reduced in GATK4. I understand…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`):
1.2.3
- OS name and version (`lsb_release -ds`):
CentOS release 6.9 (Final)
**To Reproduce**
```
bcbio_nextgen.py -n 16 sample…
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## Bug Report
I run the CNNScoreVariants as tutorial, but it can't continue and always stuck as the following picture, and the programme isn't stop by any error. By the way I can't find gatkcondaenv.…
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The current implementation if a bit messy, and we should clean it up for easier debugging and fix errors in the future.
This requires a high coverage in the class to check that nothing is gonna be …
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User has reported longer runtimes in GATK4 beta3 release compared to GATK4 beta 2 release. It sounds like this is not expected. Her runtimes are below. The first post in the forum thread has her origi…
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This user is receiving an error in their workflow when using GATK4.0.3.0. The error in the particular step can be resolved using a newer GATK version but the user has used the older version for the re…
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**Is your feature request related to a problem? Please describe.**
`snappy` currently uses an old, non-free version of GATK.
**Describe the solution you'd like**
We should mode to GATK version 4,…