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Question: Update RefSeq database with Ensembl VEP
0
Entering edit mode
17 months ago
rbagnall ♦ 1.4k
Australia

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

ADD COMMENTlink 17 months ago rbagnall ♦ 1.4k • updated 17 months ago Emily_Ensembl 18k
2
Entering edit mode
17 months ago
Emily_Ensembl 18k
EMBL-EBI

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 17 months ago Emily_Ensembl 18k
Entering edit mode
2

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 17 months ago
rbagnall
♦ 1.4k

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