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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…
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We need to pull a series of data to inform which genes to look for variants in.
There is a google doc here for reference,
https://docs.google.com/spreadsheets/d/1yX-5sfrC3vrahf4_k7-5rl4Oqzm853ol…
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We need to pull a series of data to inform which genes to look for variants in.
There is a google doc here for reference,
https://docs.google.com/spreadsheets/d/1yX-5sfrC3vrahf4_k7-5rl4Oqzm853ollI…
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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 it doesn't find a gene, etc., it doesn't say anything. Something like 'gene not found' could be more appropriate.
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**Please describe your question, suggestion, or concern.**
How is "correlated disease" used in Monarch?
I can't see where this is defined.
I had assumed it was used when a variant is correlated…
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Gene-set burden tests where the genes span multiple chromosomes are difficult to run because regenie [only supports running on a single genotype file set at a time](https://github.com/rgcgithub/regeni…
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This is currently only happening with large genes due to memory overflow on client side. A good solution to this is to cull the variant information being pulled back and optimize the data structures h…
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Dear Apex author,
I have encountered a issue in using LMM for Apex Cis/Trans
For the cis analysis, with the following commands:
```
apex cis --vcf /mnt/mfs/statgen/neuro-apex/ROSMAP-vcf/ROSMAP…
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**Please make sure that this is a bug! If you have questions about how to use TwoSampleMR please use the [Discussions](https://github.com/MRCIEU/TwoSampleMR/discussions) function instead.**
## Desc…