diff --git a/R/counts_to_snp_genes.R b/R/counts_to_snp_genes.R
index 9f28de5..0dfe340 100644
--- a/R/counts_to_snp_genes.R
+++ b/R/counts_to_snp_genes.R
@@ -158,7 +158,8 @@ write.table(merge_gene_tab, file=file_out_g, sep = "\t", quote = F, row.names =
 #
 #
 names(merge_gene_tab)[1] = "ensembl_gene_id"
-names(merge_gene_tab)[17] = "chr"
+#names(merge_gene_tab)[17] = "chr"
+colnames(merge_gene_tab)[colnames(merge_gene_tab)=="contig"] <- "chr"
 write.table(merge_gene_tab, file=file.path(opt$odir, paste0(opt$pr_name, "_processed_gene_extended2.txt")),
             sep = "\t", quote = F, row.names = F)
 #
diff --git a/python/prepare_reference.py b/python/prepare_reference.py
index c7674e8..12e2c50 100644
--- a/python/prepare_reference.py
+++ b/python/prepare_reference.py
@@ -679,7 +679,7 @@ def main():
         gzip_tabix_VCF(vcf_het)
 
         # HET VCF restrictions on the regions:
-        if (args.bed is not None or (args.gtf is not None):
+        if (args.bed is not None or args.gtf is not None):
             if (args.bed is not None):
                 vcf_het_region = vcf_het.replace(".vcf", ".selected_regions.vcf")