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**Is your feature request related to a problem? Please describe.**
We have a TODO in `_critical4protein_function` method in `src.seqvar_pvs1`. We need to properly count the pathogenic variants.
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**Is your feature request related to a problem? Please describe.**
Missense variants generally lack evidence to help determine pathogenicity.
**Describe the solution you'd like**
Add AlphaMissen…
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Right now the pipeline is set up that all HC LoF from gnomAD variants are brought into the calculations, however I would like to modify the logic so that any HC LoF variant that has a benign or likely…
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Hi Brent,
I would like to make annotated file of ExAC downloaded from [here](https://gnomad.broadinstitute.org/downloads)
`All chromosomes VCF
4.56 GiB, MD5: f2b57a6f0660a00e7550f62da2654948`
…
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**Is your feature request related to a problem? Please describe.**
We've implemented #71 . Now we need to finish it
**Describe the solution you'd like**
- Implement methods in the class
- Add un…
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Hi,
After downloading exomiser 10.0.1 and 1802_hg19 dataset, I ran the NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38 example. Everything went fine, except that in the output several v…
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We need to work out how to manage somatic classifications.
Eg How is it different from current germline ACMG in terms of scoring and evidence keys?
Dumping out notes here:
### Comment 1 ###
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@martin2urban has a list of candidate chemistry papers for curation which he will add in a comment below.
Keep curation simple, focus on take-home message in title (Tier 1 curation https://github.c…
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Running 'esm_score_multi_residue_mutations.py' gives me unrealistic results for frameshift variants.
e.g. I prepared a query for NM_000382.3 c.103delC
`MELEVRRVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDI…
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**Mondo term (ID and Label)**
MONDO:0015429 choroideremia-hypopituitarism syndrome
**Reason for deprecation**
The Orphanet ID on this is obsolete, the UMLS 'CN' id is not correct either. Seems li…