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Build breaks with many TileDB related errors:
```
In file included from /usr/ports/biology/genomicsdb/work/GenomicsDB-1.5.5-SNAPSHOT/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29:
In…
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With GATKv4.0.0.0, when I try to run GenomicsDBimport, it crashes and gives this error message:
> 19:29:01.249 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/soft.co…
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## Bug Report
### Affected tool(s) or class(es)
GenotypeGVCFs with `-all-sites`
### Affected version(s)
- 4.2 through 4.6
### Description
We tried to run GenotypeGVCFs from GATK 4.5 with …
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For GVCFs, is there a way to merge two or more existing GenomicsDBs? So that we do not need to backup in case the workspace become corrupted.
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@lbergelson, just want to discuss some issues here-
1. We currently have to use `--avoid-nio` with `--sample-name-map` and `--bypass-feature-reader` to get `GenomicsDBImport` to work with azure URI…
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This is a placeholder to
- Hold issues we are seeing with logging currently
- Collect ideas on how to improve logging.
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Hi,
We are excited about the potential to use GenomicsDB for some large cohort projects at NIH, both with GATK and for other purposes, but I am having trouble getting the build of GenomicsDB to su…
jpdna updated
6 years ago
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# Bug Report
## Affected tool(s) or class(es)
gatk `GenomicsDBImport ` `GenotypeGVCFs`
## Affected version(s)
The Genome Analysis Toolkit (GATK) v4.5.0.0
## Description
Hi,
Here is my situati…
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Hello,
Are there tools to manipulate a GenomicsDB workspace, such as removing samples? For example, can one run SelectVariants on a workspace and write the result to a new workspace?
If SelectVa…
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## Bug Report
### Affected tool(s) or class(es)
- Tool/class name(s), special parameters: GenomicsDBImport
### Affected version(s)
- Version: gatk4-4.4.0.0-0
### Description
Hel…