Hi!
First of all thank you for the great work and loftee is really helpful!
@konradjk @oleraj
I am trying to run vep-111 with LoFtee plugin (grch38) . Unfortunately I encounter the above warning even though I get no error. Following is the command I run:
vep -v \
-i results/possible_SNVs/X_VEP.vcf.gz \
--format vcf \
--cache \
--tab \
--offline \
--force_overwrite \
--buffer_size 50 \
--quiet \
--pick_allele_gene \
--assembly GRCh38 \
--dir_plugins $CONDA_PREFIX/share/ensembl-vep-111.0-0 \
--dir_cache results/vep_cache \
--custom results/gnomAD_download/gnomad.genomes.v3.1.2.sites.allchr.vcf.bgz,gnomADg3,vcf,exact,0,AF,AC,AC_XY,AN,nhomalt \
--custom results/gnomAD_download/gnomad.exomes.v4.0.sites.allchr.vcf.bgz,gnomADe4,vcf,exact,0,AF,AC,AC_XY,AN,nhomalt \
--custom results/gnomAD_download/gnomad.exomes.v4.0.sites.allchr.vcf.bgz,gnomADg4,vcf,exact,0,AF,AC,AC_XY,AN,nhomalt \
--plugin LoF,loftee_path:,$CONDA_PREFIX/share/ensembl-vep-111.0-0, human_ancestor_fa:results/loftee_data/human_ancestor.fa.gz,conservation_file:results/loftee_data/loftee.sql,gerp_bigwig:results/loftee_data/gerp_conservation_scores.homo_sapiens.GRCh38.bw \
-o stdout
PS: I installed vep and all the necessary dependencies using conda. PERL path is correctly configured.
Should I be concerned about the warning or can I simply ignore it. Any advice is highly appreciated.
Thanks in advanced.!
Hi! First of all thank you for the great work and loftee is really helpful! @konradjk @oleraj
I am trying to run vep-111 with LoFtee plugin (grch38) . Unfortunately I encounter the above warning even though I get no error. Following is the command I run: vep -v \ -i results/possible_SNVs/X_VEP.vcf.gz \ --format vcf \ --cache \ --tab \ --offline \ --force_overwrite \ --buffer_size 50 \ --quiet \ --pick_allele_gene \ --assembly GRCh38 \ --dir_plugins $CONDA_PREFIX/share/ensembl-vep-111.0-0 \ --dir_cache results/vep_cache \ --custom results/gnomAD_download/gnomad.genomes.v3.1.2.sites.allchr.vcf.bgz,gnomADg3,vcf,exact,0,AF,AC,AC_XY,AN,nhomalt \ --custom results/gnomAD_download/gnomad.exomes.v4.0.sites.allchr.vcf.bgz,gnomADe4,vcf,exact,0,AF,AC,AC_XY,AN,nhomalt \ --custom results/gnomAD_download/gnomad.exomes.v4.0.sites.allchr.vcf.bgz,gnomADg4,vcf,exact,0,AF,AC,AC_XY,AN,nhomalt \ --plugin LoF,loftee_path:,$CONDA_PREFIX/share/ensembl-vep-111.0-0, human_ancestor_fa:results/loftee_data/human_ancestor.fa.gz,conservation_file:results/loftee_data/loftee.sql,gerp_bigwig:results/loftee_data/gerp_conservation_scores.homo_sapiens.GRCh38.bw \ -o stdout
PS: I installed vep and all the necessary dependencies using conda. PERL path is correctly configured.
Should I be concerned about the warning or can I simply ignore it. Any advice is highly appreciated. Thanks in advanced.!