johnlees
commented
1 year ago lrt-pvalue is the correct column. It is probably sensible to use a Bonferroni adjustment and look at a QQ-plot. These are covered in the second part of the k-mer/LMM tutorial: https://pyseer.readthedocs.io/en/master/tutorial.html#k-mer-association-with-mixed-effects-model
AlperYurtseven
Hi, We have run Pyseer Linear Mix models using vcf files for GWAS and now we want to extract significant variant. Currently we used lrt-pvalue column and took 10 most significant variants with lowest lrt-pvalue But we are not sure if it is the right way to get significant hits. Should we consider another column? What would be your suggestions? Thank you in advance!