From ba17b78c30f6dd3bf4cc6aec89c774b3435b2beb Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@ed.ac.uk>
Date: Fri, 13 Aug 2021 11:40:47 +0100
Subject: [PATCH] Update Software_installation_ultra2.md

---
 docs/Software_installation_ultra2.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/Software_installation_ultra2.md b/docs/Software_installation_ultra2.md
index b5eb84a..38c04a1 100644
--- a/docs/Software_installation_ultra2.md
+++ b/docs/Software_installation_ultra2.md
@@ -48,6 +48,8 @@ DATE=`date +%Y%m%d%H%M`
 /home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget vep &> bcbio_install_logs/bcbio_install_datatarget_vep_${DATE}.log
 ```
 
+Q: do we even need gnomAD annotations on these? Should I be skipping VEP altogether for the alignment & variant calling pipeline?
+
 We already had gnomAD 3.0 compiled and downloaded on the ultra2 bcbio installation, so this gets copied to `/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/variation`.
 
 ```
-- 
GitLab