From 3d5e4acb50c3b3b11dfdb8ebd39a48b41b3c8347 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Fri, 14 Jun 2024 01:39:24 -0400 Subject: [PATCH] warnings file --- v03_pipeline/var/vep_config/vep-GRCh38.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/v03_pipeline/var/vep_config/vep-GRCh38.json b/v03_pipeline/var/vep_config/vep-GRCh38.json index ee350205d..4c61b73e6 100644 --- a/v03_pipeline/var/vep_config/vep-GRCh38.json +++ b/v03_pipeline/var/vep_config/vep-GRCh38.json @@ -2,7 +2,7 @@ "command": [ "bash", "-c", - "/vep --format vcf -json --hgvs --biotype --canonical --mane --minimal --numbers --regulatory --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g" + "/vep --warning_file STDERR --format vcf -json --hgvs --biotype --canonical --mane --minimal --numbers --regulatory --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g" ], "env": { "PERL5LIB": "/plugins"