The request flags VEP is asked for by default

Pure. The default for the options argument of vep_variants() and vep_variants_all(). Start from this and add to it rather than replacing it, because vcf_string is one of the identities results are matched on and mane is what vep_pick_transcript() chooses by.

Usage

vep_default_options()

Value

A named list of flags.

Supported flags

Every entry is a VEP request parameter, sent as name=value on the query string. TRUE and 1 send name=1; FALSE, 0 and NULL omit the flag. Names are case sensitive, exactly as VEP spells them. The flags this package parses are:

• AlphaMissense, mane, numbers, vcf_string: the defaults.

• af, af_gnomade, af_gnomadg: colocated variant frequencies, read by vep_parse_colocated().

• CADD, SpliceAI, REVEL: per-transcript predictor scores, read by vep_parse_element().

• hgvs: hgvsc and hgvsp notation per transcript.

• canonical: marks the canonical transcript.

• pick, pick_allele_gene: ask VEP to return one transcript per variant or per allele and gene, rather than all of them.

• protein, domains, variant_class: extra transcript annotation, carried through untouched in the response for a caller parsing it directly.

• LoF: LOFTEE, read into the lof column.

dbNSFP is refused. It returns comma-joined multi-transcript strings in dbNSFP's own order, not aligned to the transcript being reported, so the values silently belong to a different transcript than the rest of the row.

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_default_options()
#> $AlphaMissense
#> [1] 1
#> 
#> $mane
#> [1] 1
#> 
#> $numbers
#> [1] 1
#> 
#> $vcf_string
#> [1] 1
#> 
c(vep_default_options(), list(CADD = 1, REVEL = 1))
#> $AlphaMissense
#> [1] 1
#> 
#> $mane
#> [1] 1
#> 
#> $numbers
#> [1] 1
#> 
#> $vcf_string
#> [1] 1
#> 
#> $CADD
#> [1] 1
#> 
#> $REVEL
#> [1] 1
#>