https://github.com/brentp/geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.
https://github.com/brentp/geneimpacts

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prioritize effects of variant annotations from VEP, SnpEff, et al.

• Host: GitHub
• URL: https://github.com/brentp/geneimpacts
• Owner: brentp
• License: mit
• Created: 2015-07-29T21:12:07.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2024-12-10T02:58:00.000Z (6 months ago)
• Last Synced: 2025-03-31T03:09:08.831Z (3 months ago)
• Language: Python
• Homepage:
• Size: 131 KB
• Stars: 33
• Watchers: 3
• Forks: 16
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.md
  • License: LICENSE

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README

        
Given multiple snpEff or VEP or BCFTools consequence annotations for a single variant, get an orderable python object for each annotation.

[![Build Status](https://travis-ci.org/brentp/geneimpacts.svg?branch=master)](https://travis-ci.org/brentp/geneimpacts)

This is to provide a consistent interface to

different variant annotations such as from [snpEff ANN field](http://snpeff.sourceforge.net/) and the [VEP CSQ field](http://www.ensembl.org/info/docs/tools/vep/index.html).

and the [BCFTools consequence field](http://biorxiv.org/content/early/2016/12/01/090811)

This will be used in [gemini](http://gemini.rtfd.org/) but should also be of

general utility.

Design

======

There is an effect base-class and then a sub-class for `snpEff`, one for `VEP`, and one for `BCFT`

`Effect` objects are orderable (via \_\_le\_\_ ) and should have an \_\_eq\_\_ method so that we can use [functools.total_ordering](https://docs.python.org/2/library/functools.html#functools.total_ordering) to provide the other comparison operators.

Given 2 effects objects, `a` and `b`: `a < b == True` iff the *severity* of `b` is greater than `a`.

We will have a classmethod: `Effect.top_severity([eff1, ... effn]) that will return the single highest severity if that exists or

a list of the ties for highest

Rules for severity:

===================

Given 2 annotations, *a* and *b*

*a* is more severe than *b* if:

1. *b* is a pseudogene and *a* is not

2. *a* is coding and *b* is not

3. *a* has higher severity than *b* ( see below)

4. polyphen, then sift

5. ??? transcript length? (we dont have access to this).

severity

--------

Severity is based on the [impacts from VEP](http://uswest.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick)

and the [impacts from snpEff](http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf). We reduce from the 4 categories HIGH, MODERATE, LOW, MODIFIER to 3 by renaming MODERATE to MED and renaming MODIFIER to LOW.