Update RefSeq database with Ensembl VEP

Question

[rbagnall]

Hi,

I'm using the most current version of VEP (Ensembl variant effect predictor v92.3) and annotating against the RefSeq transcripts. The output shows that it is using

refseq version 01_2015

How can I update this to a more recent release? I can't seem to find where the refseq database has been installed (I'm using --offline)

Thanks

Answer 1

[Emily]

It is possible to use the VEP with a GTF/GFF file directly. If you can get an up-to-date GTF/GFF file from RefSeq, you can use this.

[rbagnall]

Thanks Emily, that worked!

For those that are interested, I got the gff file from here:

ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gff.gz

Then unzipped, sorted, bgzipped and tabix indexed, as described on the VEP link provided by Emily. This adds additional refseq annotations to my output that would otherwise be missing if I only used the -cached refseq annotations.