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.
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.
git clone https://github.com/EBIvariation/variant-remapping.git
conda env create -f conda.yml
conda activate variant-remapping
pip install -r requirements.txtDownload, manually install the following program and make sure the executable are in your PATH
Then run
git clone https://github.com/EBIvariation/variant-remapping.git
pip install -r requirements.txtRun the test script to check that you have all the right dependencies installed properly
tests/test_pipeline.shnextflow run main.nf
--oldgenome <genome.fa> \
--newgenome <new_genome.fa> \
--vcffile <source.vcf> \
--outfile <remap.vcf>--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.
--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