VEP dbNSFP plugin GRCh37

I am working with VEP and I found this interesting plugin: dbNSFP. Based on VEP instructions:

Release 3.5a of dbNSFP uses GRCh38/hg38 coordinates and GRCh37/hg19 coordinates.
To use plugin with GRCh37/hg19 data:

wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFPv3.5a.zip
unzip dbNSFPv3.5a.zip
head -n1 dbNSFP3.5a_variant.chr1 > h
cat dbNSFP3.5a_variant.chr* | grep -v ^#chr | awk '$8 != "."' | sort -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP_hg19.gz
tabix -s 8 -b 9 -e 9 dbNSFP_hg19.gz

I noticed that now the current version of the DB is 4.0.

Can I operate the same conversion as stated for the 3.5? Or shall I use this older version with less data available?

Thanks in advance for any help!

vep ensembl dbnsfp plugin anotation

• 3,154 views • link

updated 7.3 years ago by Emily

• written 7.3 years ago by cocchi.e89

Please use the code option to highlight code (10101 in the formatting bar).

• 0 views • link

written 7.3 years ago by ATpoint

1 answer

You can configure the dbNSFP plugin to use whichever version you like. However, we haven't done any testing with the new beta version and we won't start until there's a full release; from prior experience we expect this will be out in the next month or so.

• 0 views • link

written 7.3 years ago by Emily