From e84e220b52dd184a5537c1f8cf77527bf2a49802 Mon Sep 17 00:00:00 2001
From: lruizcalico <132386548+lruizcalico@users.noreply.github.com>
Date: Sun, 1 Oct 2023 18:20:52 -0700
Subject: [PATCH] Update vcf.py

Fix ref to upper
---
 src/baskerville/vcf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/baskerville/vcf.py b/src/baskerville/vcf.py
index 9e158fe..520be53 100644
--- a/src/baskerville/vcf.py
+++ b/src/baskerville/vcf.py
@@ -616,7 +616,7 @@ def vcf_snps(
                         alt_n = len(snps[-1].alt_alleles[0])
                         ref_snp = genome_open.fetch(
                             snps[-1].chr, snp_pos, snp_pos + alt_n
-                        )
+                        ).upper()
 
                         # if alt matches fasta reference
                         if snps[-1].alt_alleles[0] == ref_snp: