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stop auto-adding GT to the format field on 8-column VCFs. SVTyper adds #66

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Mar 30, 2016
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stop auto-adding GT to the format field on 8-column VCFs. SVTyper adds #66

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2 changes: 0 additions & 2 deletions svtools/vcf/variant.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,6 @@ def __init__(self, var_list, vcf, fixed_genotypes=False):
# FIXME This should be an exception
sys.stderr.write('\nError: VCF file must have at least 8 columns\n')
exit(1)
if len(var_list) < 9:
var_list.append("GT")

# make a genotype for each sample at variant
format_field_tags = var_list[8].split(':')
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