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Hii @gonzalobenegas i have some questions regarding vep.ipynb output
1. What is the threshold for scores so that we can conclude that a variant is pathogenic or not?
2. How scores are being calcul…
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- Peter's team is implementing an algorithm to detect exonic splicing enhancer mutations. I think we can try to do that, cryptic splicing, and MaxEnt analysis of the entire canonical splice site (not …
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Here's the examples from the teleconference:
[Example 1](https://gist.github.com/colinveal/63bc2b740baee4914fb2362bee967a95)
[Example 2](https://gist.github.com/colinveal/5871cb8d78765728733cbc56e55…
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There are a number of observations in the synthetic data of this form:
```
"code": {
"coding": [ {
"system": "http://loinc.org/",
"code": "69548-6",
"di…
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Our local geneticists are loo…
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**Is your feature request related to a problem? Please describe.**
Implement `PM3` and `BP2` criteria. However, no automatation exists, so it can be tricky.
**Describe the solution you'd like**
-…
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These will require additional data, so will fit well with the 14.0.0 data-upgrade theme.
- [x] PS1 - "Same amino acid change as a previously established pathogenic variant regardless of nucleotide …
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## Bug Report
### Affected tool(s) or class(es)
Funcotator
### Affected version(s)
GATK 4.1.0.0
### Description
Funcotator does not perform any annotation on a minimal VCF with canonical …
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Hello,
I would like to request that the tables used by GEMINI's built-in analysis tools be added into VCF2DB.
Ideally, all tables that are default loaded with the command:
$ gemini load
that…
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The **'Case-Control' Annotation Type** we proposed a Variant Annotation category in our initial list [here](https://docs.google.com/document/d/1csUrC4kX6G1V1GIz07btQQ3oL_cdDPJShuauL_uCjEw/edit#headin…