From 419fd8d3b3585d0088adfa8a43a554647535d93c Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@ed.ac.uk>
Date: Wed, 17 Nov 2021 08:57:35 +0000
Subject: [PATCH] Fixed peddy parsing script for ultra2
---
docs/SOP_alignment_variant_annotation.md | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/docs/SOP_alignment_variant_annotation.md b/docs/SOP_alignment_variant_annotation.md
index 5fbcec5..0994ab3 100644
--- a/docs/SOP_alignment_variant_annotation.md
+++ b/docs/SOP_alignment_variant_annotation.md
@@ -192,10 +192,11 @@ batch_id=<batch_id>
perl $SCRIPTS/trio_whole_exome_parse_peddy_ped_csv.pl \
--output ../qc/${short_project_id}_${version}.ped_check.txt \
- --project $project_id \
+ --project $short_project_id \
--batch $batch_id \
--version $version \
- --ped $PARAMS_DIR/$project_id.ped
+ --ped ../params/$project_id.ped
+ --families .
grep -v False$ ../qc/${short_project_id}_${version}.ped_check.txt
```
--
GitLab