vep-custom

Annotate variants using VEP using custom FASTA and GTF files

usage

nexus run --nf-workflow variant_annotation_vep-custom.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --vep_dir /path/to/dir/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --reference_genes_gtf_file /path/to/file.gtf \
    --reference_genes_gtf_source "GENCODE" \
    --params_vep "--species homo_sapiens --offline --cache --assembly GRCh38"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘vcf_file’.
--vep_dir	VEP cache directory.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--reference_genes_gtf_source	Reference genes GTF file source (default: GENCODE).
--params_vep	VEP parameters (default: ‘“–species homo_sapiens –database –offline –cache –assembly GRCh38”’). Note that the parameters need to be wrapped in quotes.