minos

Variant call adjudication.

Minimal instructions are below. Please see the minos wiki page for more details.

Installation

Docker

Get a Docker image of the latest release:

docker pull ghcr.io/iqbal-lab-org/minos:latest

All Docker images are listed in the packages page.

Alternatively, build your own Docker image:

sudo docker build --network=host .

Singularity

Releases include a Singularity image to download (from version 0.12.1 onwards).

Alternatively, build your own Singularity image:

singularity build minos.simg Singularity.def

From source

Dependencies:

• Python 3 (tested on version 3.6.9)
• gramtools commit 04c4ba717399507b643fd4b77a61c048ef2ed83f
• bcftools
• vt
• vcflib. Specifically, either vcflib, or all three of vcfbreakmulti, vcfallelicprimitives, and vcfuniq must be installed.
• Optionally, nextflow and ivcfmerge if you want to use the pipeline to regenotype a large number of samples.

Install by cloning this repository (or downloading the latest release), and running:

pip3 install .

Quick start

To run on one sample, you will need:

• A FASTA file of the reference genome.
• One or more VCF files of variant calls. The only requirement of these files is that they must contain the genotype field GT, and correspond to the reference FASTA file. All variants with a non-reference genotype call will be used (both alleles are considered for diploid calls)
• Illumina reads in FASTQ file(s).

For example, if you have two call sets in the files calls1.vcf and calls2.vcf, then run:

minos adjudicate --reads reads1.fq --reads reads2.fq out ref.fasta calls1.vcf calls2.vcf

where reads1.fq and reads2.fq are FASTQ files of the reads and ref.fasta is a FASTA of the reference corresponding to the two input VCF files. The final call set will be out/final.vcf.

Unit tests

Run tox to run all unit tests. They require nextflow, gramtools, vt, vcfbreakmulti, vcfallelicprimitives, vcfuniq in your $PATH.

Run an individual test file with tox tests/for_test.py::TestSpam::test_eggs.

Run the main entry point with python3 -m minos.