diff --git a/build_pop.py b/build_pop.py
index d713393668a4075b2e1e04c58598e1d0927c9a4e..7c6e70e3a42589431a6ae8570620bd944a9b0161 100755
--- a/build_pop.py
+++ b/build_pop.py
@@ -175,6 +175,8 @@ def build_genotypes_vcf_list(deletions: dict, output_vcf, haploid, force_polymor
     tabix_compress(output_vcf, output_vcf + ".gz", True)
     tabix_index(output_vcf + ".gz", force=True, preset="vcf")
 
+    os.remove(output_vcf)
+
     return genotypes_for_inds