variant-remapping

Pipeline for remapping VCF variants between two arbitrary assemblies in FASTA format. No chain file is required. However, it does assume that the source and destination genomes are closely related and was designed with the explicit purpose of lifting over variants from one version of the genome to another.

Method: creates reads from the flanking sequences of each variant, then maps them to the new assembly using minimap2.

Currently, it only SNPs and short indels but has not been tested with larger or more complex variants.

Prerequisites

To run this pipeline you will need to install and configure Nextflow version 20.7 or later. The pipeline uses other software that needs to be downloaded and installed locally. You can obtain them manually or use Miniconda.

Installation using conda

git clone https://github.com/EBIvariation/variant-remapping.git
conda env create -f variant-remapping/conda.yml
conda activate variant-remapping
pip install -r variant-remapping/requirements.txt

Installation without conda

Download, manually install the following program and make sure the executable are in your PATH

• Python
• samtools and tabix
• bedtools
• bcftools
• minimap2

Then run

git clone https://github.com/EBIvariation/variant-remapping.git
pip install -r variant-remapping/requirements.txt

Testing the installation

Run the test script to check that you have all the right dependencies installed properly

tests/test_pipeline.sh

Executing the pipeline

nextflow run main.nf 
    --oldgenome <genome.fa> \
    --newgenome <new_genome.fa> \
    --vcffile <source.vcf> \
    --outfile <remap.vcf>

Input

• --oldgenome: Old genome assembly file (FASTA format): the genome you have variants for.
• --newgenome: New genome assembly file (FASTA format): the genome you want to remap the variants to.
• --vcffile: Variants file (VCF format): contains the list of variants you want to remap.

Output

--outfile specify a VCF file containing:

• remapped coordinates (chromosome and position on the new assembly)
• the new REF alleles from the new assembly
• the ALT field possibly modified if the strand or REF has changed ID, QUAL, FILT and INFO columns of the input VCF
• Additional fields in the INFO column
• FORMAT and Sample columns if they were present in the input

Other files are created alongside the main output:

• <output>_nra_variants.vcf variants successfully remap that landed in a position where the reference allele changed. The output contains the original variant and the original reference allele as alternate.
• <output>_unmapped.vcf original variant that could not be successfully remap
• <output>_count.yml YAML file containing counts associated with each round of remapping

Configuration

The pipeline relies on Nextflow configuration to set memory and runtime requirements. This is not required for all users, but it is recommended particularly for HPC and cloud environments.

There is an example config used for tests that you can modify for your own needs. The main features are the use of labels to group processes into different categories based on their resource needs (small/medium/large), and the use of base_memory and base_time variables that some processes use to fine-tune their requirements.

For more about Nextflow configuration, see the documentation.