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**Describe the bug**
I saved my own recessive permissive search (using the criteria for recessive permissive in the RGP workflow) and tried to look for the "answer" to case 0985 in Exome Project L (c…
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ACMG uses as evidence of pathogenicity the fact that a particular variant is nonsense coupled with the fact that LOF variants are known mechanisms of disease. We need a set of terms to use for mechan…
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bcbio + crg pipeline uses vcfanno config from `~/crg/crg.vcfanno.conf` and `/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/config/vcfanno/gemini.conf`
but crg2 has been using …
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Tthere are `1919` pathogenic variants (from `biallelic_by_tumortype_merge.txt` and `mutations_cnv_by_tumortype_merge.txt`).
None of them are in`signaldb_variants_by_cancertype_summary_statistics.txt`…
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On Variant Details page we should show:
* variants on the same codon.
* same exon or +/- X AA away
* Same protein domain
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Very useful for ACMG classifications involving hotspot…
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Here are the first round reviews from the Pathogenesis Manuscript as an itemized list and the full text:
- [x] Reviewer 1.1
- [ ] Reviewer 1.2
- [ ] Reviewer 1.3
- [ ] Reviewer 1.4
- [ ] Reviewer…
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195-1 | In tiering variants gets annotated to AC092143.1 and TUBB3 (overlapping Ensembl genes) and latter results in a tier 2 diagnosis on latest ID panel. For Exomiser gets former only and this ha…
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What are the values for this?
Is it something like:
Pathogenic Very Strong
Pathogenic Strong
...
Benign Strong
Not Applicable?
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* Need to write an exporter from SA Path - might as well write as current export format
* Write an importer for current export format, can then move tags around systems.
Do as part of http://github.…
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As mentioned by Heidi Rehm during her [talk](https://drive.google.com/file/d/1EVc1aOKS1OrM0tgRcxDKOHwzqpNPAhuF/view) at the recent Genomics of Rare Disease Conference, the [AnVIL](http://anvilproject.…