Question: Update RefSeq database with Ensembl VEP
0
gravatar for rbagnall
2.0 years ago by
rbagnall1.6k
Australia
rbagnall1.6k wrote:

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

refseq vep ensembl • 1.2k views
ADD COMMENTlink modified 2.0 years ago by Emily_Ensembl20k • written 2.0 years ago by rbagnall1.6k
2
gravatar for Emily_Ensembl
2.0 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

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.

ADD COMMENTlink written 2.0 years ago by Emily_Ensembl20k
3

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.

ADD REPLYlink written 2.0 years ago by rbagnall1.6k
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