Question: VEP dbNSFP plugin GRCh37
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gravatar for cocchi.e89
7 months ago by
cocchi.e8930
cocchi.e8930 wrote:

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!

ADD COMMENTlink modified 7 months ago by Emily_Ensembl19k • written 7 months ago by cocchi.e8930
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Please use the code option to highlight code (10101 in the formatting bar).

ADD REPLYlink written 7 months ago by ATpoint26k
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gravatar for Emily_Ensembl
7 months ago by
Emily_Ensembl19k
EMBL-EBI
Emily_Ensembl19k wrote:

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.

ADD COMMENTlink written 7 months ago by Emily_Ensembl19k
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