feat: code to subset the ensembl gtf added

2025-09-09 11:50:40 +02:00
parent 485c1ea0b5
commit 2a9a240e8a
1 changed files with 7 additions and 0 deletions
--- a/gene_bed.sh
+++ 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
+