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## Describe the issue
Hello, I'm testing v113 using the v113 docker obtained from docker hub and the v113 cache downloaded using the following command:
`docker run --network host -t -i -v /mnt/data1…
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According to the [nomenclature pages](http://varnomen.hgvs.org/recommendations/general/), the pipe is used for:
> (...) indicate that not a direct change of the sequence is described but a modificati…
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When converting c. HGVS from cDNA to genome coordinates, VEP appears to not take into account alignment gaps, where the cDNA has insertions/deletions vs the reference sequence.
Submission example:
…
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Hi guys,
I get regular requests from collaborators to look if we have seen germline variants in a specific gene within our AFHCS or GA cohorts. I've created a 'Gene Search' analysis to have a quick…
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Hi:
Is there any way to disable the mail notification for variant analyses? Today I performed roughly 90 variant analyses from the genomic variants tab and hours after everything was done, I sudden…
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> Advanced machine learning models applied to large-scale genomics datasets hold the promise to be major drivers for genome science. Once trained, such models can serve as a tool to probe the relation…
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Add a module to filter variants post-merge in bulk pipeline.
I've typically used the following:
```
vcftools --gzvcf ${MY_VCF} \
--max-missing 1.0 \ # may want to lower this
--min-alleles 2…
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From https://github.com/monarch-initiative/monarch-app/issues/1224: "take care in dipper to exclude inclusion of derived assertions that are redundant with a source we already bring in".
Issue report…
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### Need
As a clinician I want to be able to detect all true somatic variants, but currently in WGS-tumor-only cases we are filtering out all somatic variants with a VAF of 1 with a bcftools filter…
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For instance if you have a translocation from chrA:posA to chrB:posB and chrC:posC, only translocation from chrA:posA to chrB:posB is loaded as a variant
Of course this happens more often in cancer…