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via @jxchong cc @arq5x
A user may find a variant that is not itself associated with disease, but is in a gene known to be associated with the disease. There is no way to store or query this info in g…
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Hello,
For gene-based analyses, I was wondering if it was possible to set a minimum allele count? For instance, I want to build bins using MAF < 1% and for the MAC to be at least 10 variants. Addit…
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I have few upstream gene variants. But looks like there is no such/similar annotation in the `variant_classification_filter` column. So, not sure what annotation to put there?
any suggestions?
I a…
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Suggestions by @vwirta :
- Type of causative vars (snv/SV) and the specific subcategory (frameshift, stop codon etc.)
- Compounds
- Clinvar classification of our causatives
- Population frequen…
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I use these all the time when working directly against gemini.
http://gemini.readthedocs.org/en/latest/content/querying.html#gt-filter-filtering-on-genotypes
For example:
```
gemini query --header…
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@julesjacobsen given the lack of strictness in the semantics of version 1 variants, it seems it might be better to emit a warning here that the user will need an implementation specific way of doing t…
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Al - Do you know if there are any issues with the ClinVar annotations? I just pulled up proband .....52 in study A259. I had this listed as a stop gain, clinvar variant in SCN8A, but I'm not seeing an…
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When reviewing variants, it is important to be able to evaluate the role of the variant, but also how well the gene matches to the entered phenotypes. I imagine 2 things to do:
1. In the variant re…
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Hi,
I am using the GENESIS package to perform a SKAT-O analysis on every chromosome, variants being aggregated by genes.
I am using the same code for all of the chromosomes, and it worked perfectl…
pjuge updated
11 months ago
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Currently we infer human gene to phenotype annotations by making the join
gene - disease (through a variant)
disease - phenotype
With some minor filtering of gene disease associations for marker…