From b2f10bb5e0e4416fb4af43914bcbfb47e3c721bc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?M=C3=BCck?= <m991k@b260-pc003.inet.dkfz-heidelberg.de>
Date: Sat, 1 Jun 2024 15:42:20 +0200
Subject: [PATCH] Regenerate IDs for VEP annotation inout VCFs

---
 pipelines/annotations.snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipelines/annotations.snakefile b/pipelines/annotations.snakefile
index fa3b1d0f..90c0dfcc 100644
--- a/pipelines/annotations.snakefile
+++ b/pipelines/annotations.snakefile
@@ -299,7 +299,7 @@ rule strip_chr_name:
     output:
         anno_tmp_dir / "{file_stem}_stripped.vcf.gz",
     shell:
-        f"{load_hts} cut -c 4- {{input}} |bgzip > {{output}}"
+        load_hts + """ cut -c 4- {input} | awk -F'\\t' 'BEGIN {{OFS = FS}} {{$3 = "chr"$1"_"$2"_"$4"_"$5; print}}' |bgzip > {output} """
 
 
 rule vep: