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normalize effects from variant annotation tools (snpEff, VEP)

Project description

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

[![Build Status](](

This is to provide a consistent interface to
different variant annotations such as from [snpEff ANN field]( and the [VEP CSQ field](
and the [BCFTools consequence field](

This will be used in [gemini]( but should also be of
general utility.


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]( 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 serverity 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 is based on the [impacts from VEP](
and the [impacts from snpEff]( We reduce from the 4 categories HIGH, MEDIUM, LOW, MODIFIER to 3 by renaming MEDIUM to MED and renaming MODIFIER to LOW.

Project details

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