index file after fixing

atgu · Feb 3, 2025 · 4178cc1 · 4178cc1
1 parent c125e58
commit 4178cc1
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/gwaspy/check_alleles/check_alleles.py b/gwaspy/check_alleles/check_alleles.py
@@ -88,6 +88,7 @@ def fix_alleles(
         j.command(
             f"""
             bcftools +fixref {vcf['vcf']} -Ob -o {j.fixed_file['bcf']} -- -f {ref_fasta['ref_fasta']} -m {allele_mode}
+            bcftools index --force {j.fixed_file['bcf']} --output {j.fixed_file['bcf.csi']} --threads {ncpu}
             """
         )