Build the variant key VEP results are matched on

Pure. vep_variants() returns a key column built this way, so this is what a caller uses to join the result back onto its own variant table.

Usage

vep_key(chrom, pos, ref, alt)

Arguments

chrom

A chromosome, with or without a chr prefix.

pos

A 1-based position.

ref, alt

Reference and alternate alleles.

Value

A single string, chrom-pos-ref-alt.

References

McLaren et al. (2016). The Ensembl Variant Effect Predictor. Genome Biology 17, 122. doi:10.1186/s13059-016-0974-4

Service documentation: https://rest.ensembl.org/

Examples

vep_key("7", 140753336, "A", "T")
#> [1] "7-140753336-A-T"
vep_key("chr7", 140753336, "a", "t")
#> [1] "7-140753336-A-T"