From 2a9a240e8a23c1753cc1169d756a03e614d5f8eb Mon Sep 17 00:00:00 2001
From: Darren Wight <darren@serenomica.com>
Date: Tue, 9 Sep 2025 11:50:40 +0200
Subject: [PATCH] feat: code to subset the ensembl gtf added

---
 gene_bed.sh | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 gene_bed.sh

diff --git a/gene_bed.sh b/gene_bed.sh
new file mode 100644
index 0000000..798291d
--- /dev/null
+++ b/gene_bed.sh
@@ -0,0 +1,7 @@
+zcat Homo_sapiens.GRCh38.115.gtf.gz \
+	| awk '{if ($3 == "gene") {print $0}}' \
+	| grep -E 'gene_name \"BRCA1\"|gene_name \"PALB2\"|gene_name \"CHEK2\"|gene_name \"ATM\"' \
+	| gff2bed - \
+	| sort -k1,1 -k2,2n \
+	> test.bed
+