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Merge pull request #110 from Illumina/issue_109
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Added missing bcftools invocation to command line for region processing
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dskola authored Feb 13, 2020
2 parents 46ee23c + ec8172c commit 9d128a9
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion src/python/Tools/bcftools.py
Original file line number Diff line number Diff line change
Expand Up @@ -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:
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