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VEP on non-toplevel coords

Marek Szuba requested to merge github/fork/willmclaren/master into master

Created by: willmclaren

Adding in some code and supporting stuff to allow the VEP endpoints to deal with input on non-toplevel coords; specifically this is targetted at input on alt haplotypes, e.g.


On previous versions this just returns an intergenic result, which is misleading as a) there's no error generated since the slice fetch test passes and b) if you transform to toplevel you do get consequences:

[ { assembly_name: "GRCh38", end: 32582565, seq_region_name: "CHR_HSCHR6_MHC_MANN_CTG1", strand: 1, transcript_consequences: [ { variant_allele: "G", hgnc_id: "HGNC:4948", strand: -1, gene_symbol: "HLA-DRB1", transcript_id: "ENST00000411959", gene_id: "ENSG00000227826", biotype: "protein_coding", gene_symbol_source: "Uniprot_gn", consequence_terms: [ "intron_variant" ], impact: "MODIFIER" }, etc etc

There is a small issue in that the returned coordinates are then different to the input, but there's no real way around this.

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