Merge pull request #110 from Illumina/issue_109

Added missing bcftools invocation to command line for region processing
Illumina · Feb 13, 2020 · 9d128a9 · 9d128a9
2 parents 46ee23c + ec8172c
commit 9d128a9
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/python/Tools/bcftools.py b/src/python/Tools/bcftools.py
@@ -235,7 +235,7 @@ def preprocessVCF(input_filename, output_filename, location="",
                 vargs += ["-o", tff.name, "-O", "b"]
                 runShellCommand(*vargs)
                 runShellCommand('bcftools', "index", tff.name)
-            vargs = ["view", tff.name, "-R", regions]
+            vargs = ["bcftools", "view", tff.name, "-R", regions]
 
         if somatic_allele_conversion:
             if type(somatic_allele_conversion) is not str: