Polymorpheus

Integrated toolkit with web GUI for analysing genetic polymorphisms and their potential effects.

The software takes a VCF file with the genetic variants, annotates it and allows browsing the results in a user-friendly manner.

It uses SnpEff for annotating the VCFs.

Setup

Download the repository:

$ git clone https://github.com/mzdravkov/polymorpheus.git

Alternatively, you can download a zip archive by visiting https://github.com/mzdravkov/polymorpheus then clicking on Code->Download ZIP. Then decompress it.

Go to the root directory of the repository:

$ cd gene_variants

Download SnpEff (If you already have SnpEff, you can use your existing installation. See the note below.):

# Download the latest version
$ wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip -O SnpEff.zip

# Unzip the files
$ unzip SnpEff.zip

Note: If the installation directory of SnpEff is not polymorpheus/snpEff you'll have to change the property snpEff_path in config.yaml to the correct directory

Create a virtual environment and install dependencies:

$ python -m venv env
$ source env/bin/activate
$ pip install -r requirements.txt

Running

To run the web app:

$ python src/run_app.py

Then visit the application on http://127.0.0.1:5000/.

Usage

Gene sets

Polymorpheus uses the concept of gene sets to specify which genes you're interested in analysing. You can define a gene set by uploading a file with HGNC gene names. Subsequently, when you upload a VCF file you specify which gene set you wish to analyse it against. Polymorpheus will extract polymorphisms from the VCF only for the genes in the gene set.

Browsing parsed VCFs

When you upload a VCF file, Polymorpheus will use SnpEff to annotate it.

Note: The first time you process a VCF that uses a reference genome that hasn't been used before, SnpEff will automatically download it. This may take a few minutes.

Once the VCF is marked as processed then Polymorpheus has already annotated, filtered, parsed and stored the data in a local database for fast access to the data. You can browse the information for the polymorphisms in the VCF, this includes:

• Listing affected genes with information on their function and processes they participate in.
• Listing genetic variants with their predicted effect for a given gene. You can filter them by various properties.
• Embedded genomic browser, showing the variants, transcripts and genes.
• Finding how a polymorphism modifies the protein sequence.