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Implement @zmartine's proposal to enhance SnpEff's default impact values for each variant with a new "predicted impact" that accounts for significant changes in hydrophobicity, etc.
Input:
- _VCF fil…
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Right now we have it set at 50bp. Idan says 250 is more typical for bacteria and yeast.
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Hi,
Many thanks to the developers.
I used use the mutmap v2.3.3 and showed "MutMap successfully finished". But the message "SystemError: tile cannot extend outside image" showed in the last line. I…
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Will including this config file (licensed under LGPLv3) cause any conflict with our current licensing?
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Hi,
I was able to use the Smoove population SV calling pipeline to SV call 200+ samples.
SVs that we are interested in were also included in the results.
So the pipeline worked fast and the re…
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Right now snpeff download its database at run time. And on top of that it installs it in the `CONDA_PREFIX` folder
There are at least three cases where this will crash the pipeline.
1- When the pi…
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# Key specs for the MVP1
- [x] Have as many species as possible listed in https://brc-analytics.org/data/organisms
- [ ] Have all species from above registered as Galaxy Reference data with corre…
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**Describe the bug**
Put the variant `GRCh37:17:41197726:AG:A` as VCF. Annotate with SnpEff and `GRCh37.p13`. See that it is predicted to be stop_gained for NM_007294.4. Compared with VariantValidato…
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Create different kind of parser
- [x] Raw VCF
- [x] VEP
- [x] SnpEff
- [ ] Annovar
- [ ] Affymetrix
- [ ] MAF format
- [ ] Varank format
dridk updated
2 years ago
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https://github.com/NBISweden/GenErode/blob/main/workflow/rules/9_merge_vcfs.smk#L266C23-L266C42
This command does not remove sites that are coded as heterozygous sites but are fixed derived sites (…
verku updated
3 months ago