vcf GT format:0/0, 1/1 or 0 , 1

[yayahoho1]

Hi,
i am using pyseer to do GWAS analysis in bacteria. But i am not sure whether the vcf GT format would make a difference to the result?
The vcf file was generated from snippy sofware.

tkanks in advance !

[johnlees]

The code for this is here: https://github.com/mgalardini/pyseer/blob/master/pyseer/input.py#L445-L490
See the comment on lines 471-474:

          # This is dominant encoding. Any instance of '1' will count as present
          # Could change to additive, summing instances, or reccessive only counting
          # when all instances are 1.
          # Shouldn't matter for bacteria, but some people call hets

So any 1 in the GT field should count as present