GWAS in bacteria without phenotype and trait details

How to run PLINK --assoc for bacteria isolates in each lineage with high or low transmissibility information.

The *.fam file in the format :

Lineage (single) mapping - 0 -9
Lineage (single) mapping - 0 -9

Generated bed,bim,fam,map with the option missing phenotype

I have the lineage specific *.vcf files (for high and low transmissible) ,snp for each lineage and its gene details.

Any advice would be great.

Thanks

genome snp

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updated 4.9 years ago by Ram

• written 11.4 years ago by cloud15 •

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