https://github.com/edawson/fe

A python script/minimal GUI app for aggregating variant annotations and predicting impacts
https://github.com/edawson/fe

Last synced: 3 months ago
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A python script/minimal GUI app for aggregating variant annotations and predicting impacts

• Host: GitHub
• URL: https://github.com/edawson/fe
• Owner: edawson
• Created: 2017-11-08T16:27:23.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2018-02-28T15:37:59.000Z (over 7 years ago)
• Last Synced: 2025-01-07T20:47:10.273Z (5 months ago)
• Language: Python
• Size: 10.7 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
fe

----------

Eric T Dawson  

October 2017

### Introduction

fe is a single python script that annotates VCF variants with predicted functional impacts.

These come from an aggregated database (dbNSFP) containing variant effect predictions from

multiple tools and optionally from the raw output of bcftools csq (a fast, phase-aware VEP clone from Petr Danecek).

Bedtools (Aaron Quinlan + others)  is used to sort and intersect VCF files.

### Installation

fe requires wooey (a python web app framework), pytabix, pyensembl, bedtools and bcftools.

### Usage

        python scan.py -i my_vcf.vcf -t tabixFI.gz

### Getting help

post on [github](https://github.com/edawson/fe) for bugs and help!