Variant call adjudication.

Dependencies:

• Python 3 (tested on version 3.6.9)
• gramtools commit 9313eceb606a6fc159e4a14c168b7a6f888c5ed2
• 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 .

Alternatively, instead of running pip3, build a Singularity container by running:

singularity build minos.simg Singularity.def

Supposing you have variant calls for one sample, called by two different tools in the files calls1.vcf and calls2.vcf. 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.

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.