varifier

Note: full documentation is under construction.

If you use Varifier, please cite: https://doi.org/10.1186/s13059-022-02714-x

Installation

conda

Prerequisite: conda (and bioconda channel correctly set up)

$ conda install varifier

Container

Docker images are hosted at quay.io.

singularity

Prerequisite: singularity

$ URI="docker://quay.io/iqballab/varifier"
$ singularity exec "$URI" varifier --help

The above will use the latest version. If you want to specify a version/commit then use a tag (or commit) like so.

$ TAG="3c8152a"
$ URI="docker://quay.io/iqballab/varifier:${TAG}"

docker

Prerequisite: docker

$ docker pull quay.io/iqballab/varifier
$ docker run quay.io/iqballab/varifier varifier --help

You can find all the available tags on the quay.io repository.

Local

Dependencies:

• Python 3 (tested on version 3.6.9)
• mummer installed
• paftools.js and k8 in your path. See https://github.com/lh3/minimap2/tree/master/misc

Install:

pip3 install .

Usage

To verify calls in a VCF file, you will need:

1. test.vcf - the VCF file to be tested
2. ref.fasta - FASTA file of reference corresponding to the VCF file
3. truth.fasta - a truth genome FASTA file

Run:

varifier vcf_eval truth.fasta ref.fasta test.vcf out_dir

This makes a new directory called out_dir. The results are in the file summary_stats.json.

Tests

To run the tests, run tox from the root of the repository.