From d238d202a145d369c7f5c4806059ef8becf1a0de Mon Sep 17 00:00:00 2001 From: Dave Larson Date: Tue, 29 Mar 2016 16:09:15 -0500 Subject: [PATCH] stop auto-adding GT to the format field on 8-column VCFs. SVTyper adds this itself and is the only place we think this matters. Closes #59. --- svtools/vcf/variant.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/svtools/vcf/variant.py b/svtools/vcf/variant.py index f2c951f0..8c78148f 100644 --- a/svtools/vcf/variant.py +++ b/svtools/vcf/variant.py @@ -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(':')