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 hall-lab#59.
ernfrid · Mar 29, 2016 · d238d20 · d238d20
1 parent d4cb742
commit d238d20
Showing 1 changed file with 0 additions and 2 deletions.
diff --git 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(':')