From 15f1e1b27faf994a9180bc3af1250863ee5160a0 Mon Sep 17 00:00:00 2001 From: ameyner2 <alison.meynert@ed.ac.uk> Date: Mon, 23 Aug 2021 13:44:56 +0100 Subject: [PATCH] Fixed a couple of resource paths --- docs/Setup_variant_prioritization.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/Setup_variant_prioritization.md b/docs/Setup_variant_prioritization.md index 4b2e9e5..fbb542a 100644 --- a/docs/Setup_variant_prioritization.md +++ b/docs/Setup_variant_prioritization.md @@ -39,8 +39,6 @@ Location at EPCC: /home/u035/u035/shared/software/bcbio/anaconda/share/ensembl-v File name: G2P.pm -Backup: gitlab.ecdf.ed.ac.uk/igmmbioinformatics/trio-whole-exome/resources - ### Add splice region variants (1-3 bases of the exon or 3-8 bases of the intron) for consideration by G2P Edit the G2P.pm file by adding the type `splice_region_variant` at the end of: @@ -146,7 +144,7 @@ Source: https://www.ebi.ac.uk/gene2phenotype/downloads Date obtained: 06/07/2021 -Location at EPCC: /home/u035/u035/shared/resources +Location at EPCC: /home/u035/u035/shared/resources/G2P File names: DDG2P.20210706.csv and genes_in_DDG2P.20210706.txt @@ -194,7 +192,7 @@ Found 3553 unique gene names (incl.synonyms) in DDG2P.20210706.csv recorded 3553 unique gene names (incl. synonyms); outfile = genes_in_DDG2P.20210706.txt ``` -* Copy `genes_in_DDG2P.<date_downloaded>.txt` from `<eddie_work_folder>` to `<datastore_work_folder>` and to ultra at /home/u035/u035/shared/resources +* Copy `genes_in_DDG2P.<date_downloaded>.txt` from `<eddie_work_folder>` to `<datastore_work_folder>` and to ultra at /home/u035/u035/shared/resources/G2P * After updating the DDG2P list, update the resources for coverage analysis, see below: * CCDS Dataset (check if updated CCDS is available) * DD genes Dataset -- GitLab