diff --git a/vcf/parser.py b/vcf/parser.py index c3c3d08..5b787c7 100644 --- a/vcf/parser.py +++ b/vcf/parser.py @@ -478,6 +478,8 @@ def _parse_samples(self, samples, samp_fmt, site): # short circuit the most common if samp_fmt._fields[i] == 'GT': sampdat[i] = vals + if vals == ".": + sampdat[i] = None continue # genotype filters are a special case elif samp_fmt._fields[i] == 'FT':