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mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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vcf GT format:0/0, 1/1 or 0 , 1 #241

Open yayahoho1 opened 1 year ago

yayahoho1 commented 1 year ago

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 commented 1 year ago

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