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21 days ago
DareDevil
★
4.4k
I'm trying to annotate a VCF file with AlphaMissense scores using VEP in offline mode with the dbNSFP v5.1a database (GRCh38 build). I’ve downloaded the dbNSFP.1a_grch38.gz file from the official academic Google Drive link under the folder dbNSFP_for_VEP_SnpSift, and extracted it for use with VEP.
the command I’m running:
vep --offline --cache --assembly GRCh38 \
--input_file homo_sapiens_GRCh38.vcf --output_file my.output.vep.vcf --vcf \
--dir_cache ~/.vep --fasta ~/.vep/homo_sapiens/113_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
--plugin dbNSFP,/media/molmed/Analysis/ensembl-vep/dbNSFP/dbNSFP5.1a_grch38,AlphaMissense_score,AlphaMissense_rankscore,AlphaMissense_pred \
--fork 12 --dir_plugins /media/molmed/Analysis/ensembl-vep/dbNSFP
But I am getting following error:
WARNING: Failed to compile plugin dbNSFP: Can't locate dbNSFP.pm in @INC (you may need to install the dbNSFP module) (@INC contains: /media/molmed/Analysis/ensembl-vep/dbNSFP /media/molmed/Analysis/ensembl-vep/modules /media/molmed/Analysis/ensembl-vep /home/molmed/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/molmed/perl5/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at (eval 37) line 2.
BEGIN failed--compilation aborted at (eval 37) line 2.