Fix genotype svtyper rule

snakecnv/bin/svtyper_launcher.py

@@ -36,7 +36,8 @@ def launch(bamlist, input_vcf, output_vcf, threads):
                                       vcf_in=input_vcf,
                                       vcf_out=vcf_out,
                                       cores=threads)
-            if run("bcftools sort -O z -o {ovcf} {ivcf}".format(ivcf=vcf_out, ovcf=output_vcf)).returncode == 0:
+            if run("bcftools sort -O z -o {ovcf} {ivcf}".format(ivcf=vcf_out, ovcf=output_vcf), shell=True)\
+                    .returncode == 0:
                 os.remove(vcf_out)
                 tabix_index(output_vcf, force=True, preset="vcf")
             else: