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1 parent e8c1f4e commit 3c3999bCopy full SHA for 3c3999b
python/runNanoSeq.py
@@ -1208,8 +1208,8 @@ def vcfHeader(args):
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cmd = "cp %s merged.vcf.gz ;"% vcf2Merge.pop(0)
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for ifile in vcf2Merge[1:]:
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cmd += " bcftools concat --no-version -Oz -o tmp.xxx.vcf.gz merged.vcf.gz %s; mv tmp.xxx.vcf.gz merged.vcf.gz; "%ifile
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- cmd += "; bcftools sort -Oz -o %s/post/%s.indel.vcf.gz merged.vcf.gz" % (tmpDir, args.name)
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- cmd += ";bcftools index -t -f %s/post/%s.indel.vcf.gz " % (
+ cmd += "bcftools sort -Oz -o %s/post/%s.indel.vcf.gz merged.vcf.gz;" % (tmpDir, args.name)
+ cmd += "bcftools index -t -f %s/post/%s.indel.vcf.gz " % (
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tmpDir, args.name)
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runCommand(cmd)
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