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GenomicsDBImport currently doesn't support multi-sample input vcfs. We've had a number of usesr request the ability to import precombined multi-sample vcfs.
People may have old call-sets which t…
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## Bug Report
### Affected tool(s) or class(es)
Reblock | JointGenotype
### Affected version(s)
- [x] Latest public release version [version?]
- [ ] Latest master branch as of [date of test?]…
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Hello,
When I use GenomicsDBImport and GenotypeGVCFs , I get the following error: Couldn't create GenomicsDBFeatureReader, I have no problem with running CombineGVCFs with CombineGVCFs.
I referenc…
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I want to run GATK on an arm machine, and I did these:
1. compile the source code of GenomicsDB
2. generate the shared library: libtiledbgenomicsdb.so
3. insert the shared library into the JAR pack…
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## Feature request
### Tool(s) or class(es) involved
GenomicsDBImport and GenotypeGVCFs (and other tools that can take GenomicsDBs as input)
### Description
Could it be possible to add support…
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I have combined some GVCFs by GenomicsDBImport, and continuity added other samples. however, I find some mistakes with previous samples, how to delete these samples from GATK GenomicsDBImport?
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## Bug Report
### Affected tool(s) or class(es)
GenomicsDBImport
### Affected version(s)
Latest
### Description
Output from GenomicsDBImport is sorting based on alphabetic order: chr 10 a…
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I am wondering would it possible to query the data based on the other columns rather than chromosomal coordinates? For example based on the GT or BaseQRankSum.
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### Description of the bug
Dear All, I am facing a problem almost at the end of sarek version 3.1 for germline detection.
Could you please provide me assistance and help me to fix it?
Many Th…
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Hi,
I've been hitting errors when running some tests of germline small variant joint calling with GATK (trying to optimise some parameters for running on our cluster).
First there were I/O error…