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Hello, bcbio community!
Thanks for the great framework!
Gnomad_genome frequencies help to prioritize variants in WGS studies.
However, it would be nice to have functional prediction and conserv…
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**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.1
- OS name and version: Ubuntu 18.04.4 LTS
**To Reproduce**
- cd /work/manager/NA12878-exome-eval/work
- bcbio_nextgen.py…
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Related to: #82
Config and files used are arbitrary, just make a typo in the path for `file` in config toml and `-base-path`.
When attempting to open a Source file, the basepath is prepended tw…
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Hi bred!
I have a suggestion for your already amazing vcfanno.
When annotating AF from an external file (gnomAD for example) it would be more convenient to have the annotation field set to zero …
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I'm running the pipeline on a practice AshkenaziFam dataset before trying it on my own data. I'm having trouble getting the AshkenaziFam-ensemble.db file at the end of my run. Previously, I was runn…
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Hey guys!
Thanks for the great pipeline!
Has anybody checked the precision of RNA-seq variant calling since the introduction of gatk4?
Previously, with gatk 3x after rna-editing filtration it w…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.3
- OS name and version (`lsb_release -ds`): "CentOS Linux release 7.6.1810 (Core) "
**To Reproduce**
Exact bcbio command you…
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## Description
Rerun cases set to analyze sometimes will not start for several days
This is because decompression logic fails to add the files to Housekeeper at one of the steps
Needs more invest…
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Hi!
when running variant calling on hg38 with disambiguate on mm10:
```
details:
- algorithm:
aligner: bwa
coverage: /path/coverage.bed
coverage_interval: regional
disambig…
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**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.3
- OS name and version: Ubuntu 19.10
**To Reproduce**
bcbio_nextgen.py upgrade -u development --tools --data
**Observed b…