sydelstan

does the continuous trait need to be normally distributed? is there a test to confirm the assumptions of the OLS are met?

The output returns sites with variants that are significantly associated with a phenotype, the samples in which the variants are found, and the lineage the variant is most associated with....

Yes by ‘expressed’ I mean ‘present’ I attached a screenshot. The variants in column B are presents in the samples in column J. Column I says that the variants in...

I've included three lineages, and I used the --lineage-clusters option. I'm still not sure why the variants would be associated with a lineage where no strains express that variant

[BDQ_CA_lineage.txt](https://github.com/mgalardini/pyseer/files/7543117/BDQ_CA_lineage.txt)

Great, I'll try that

I have read the great wiki article by @MrTomRod but I am still not sure how to understand the situation described by @plasmid02

I have the same error as @hollygene when using the -n option but I am not sure why that is the case @mgalardini @AdmiralenOla

I ran the same lines with v2.6.5 and I ended up with even more strains included in the cytoscape network. Am I calling the correct reference database and network file?...

> It would also help if you could let me know the numbers of files included in the database, visualisation and subset file; and also give an example of a...