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When I execute the script STAARpipelineSummary_Known_Loci_Pruning.r, there are several chromosomes that did not generate corresponding data, and the error is as follows:
used (Mb) gc trigger…
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New term request Glycogen brancher enzyme activity low in skin fibroblast (segal_090511164419): GBE; Amylo(1,4 - 1,6) transglucosidase deficiency UMLS: 1856314
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**Mondo term (ID and Label):**
MONDO:0011965 familial temporal lobe epilepsy 2
**Xref that should be fixed (ID and label):**
[Familial temporal lobe epilepsy](https://www.ebi.ac.uk/ols4/ontologie…
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There are a few SNPs with pathogenic WT alleles:
- chr2:27508073-27508073 T>C (GCKR, Fettleber) - AF67%
- chr2:27518370-27518370 T>C (GCKR, Fettleber) - AF66%
- chr7:87450090-87450090 T>A (ABCB4, chol…
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Hi,
I have tried to score the examples in the README using PhenoSV-light, but the Phen2Gene and PhenoSV scores are always 0. What could be the reason for this?
I would appreciate your guidance.…
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Hi Lindsay,
I noticed that in the paper you stated "A variant is predicted to be an eQTL or GWAS hit if its log-odds is greater than 0.01 (eQTL) or 0.0075 (GWAS) ". However, in the CharacterizeVari…
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Hi,
When I'm running this step in https://deeprvat.readthedocs.io/en/latest/annotations.html#running-the-pipeline:
```
(deeprvat_annotations) pichuan@pichuan-gpu:~/deeprvat/example/annotation…
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Curated by @jingluodatacurator
https://canto.phi-base.org/curs/fa6dafc2380a5876
Notes:
Uniprot IDs: G4XX47, G4XX53, G8EI90
~Strains~ Genes/proteins: SdhB, SdhC, SdhD (see Table 3 and Table 4)…
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Hi Xihao,
1)
I see a lot of these warnings in my analysis and my cohort is very small, ~480 samples.
Would it be safe to use single.strand.genes.only=FALSE to increase the # variants in a gene…
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**Describe the bug**
Alba first called a translocation involving HOXA13. I searched and tagged it in seqr - https://seqr.broadinstitute.org/project/R0384_rare_genomes_project_gen/saved_variants/varia…