Giter Club home page Giter Club logo

biol68412's Introduction

Repository for code and extra materials for the Advanced Clinical Bioinformatics (BIOL68412) Assignment.

Files

  • Cardiac_Transcripts.bed
    • BED file of genes and transcripts used
  • Cardiac_Targets.bed
    • BED file of targets used for analysis. Created using HyperDesign, all exon targets have a 15bp overhang
  • Filter_Annotation.py
    • Python script to filter the VEP output

Requirements for Filter_Annotation.py

  • Python3
    • openpyxl module installed

Running Filter_Annotation.py

  1. Download VEP output in txt format
    • Ensure RefSeq transcripts were used in VEP
    • Ensure gnomAD allele frequencies were included
  2. Place VEP txt output in the same location as Filter_Annotation.py and Cardiac_Transcripts.bed
  3. Run the script using the -f flag to specify the input file name e.g:
    • python3 Filter_Annotation.py -f VEP_output.txt
  4. The output file will be named based on the input file e.g:
    • If the input filename was VEP_output.txt the filtered annotation file will be named VEP_output_FILTERED.xlsx

biol68412's People

Contributors

kjthoward avatar

Watchers

James Cloos avatar avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.