leoisl/varifier

Variant call verification

varifier

This is the repository used to retrieve the the truth variants from a set of genomes to get pangenome variations in the pandora paper.

To build the container for the paper: cd containers && ./build_container_for_paper.sh

Installation

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.