pyseer_gwas
Standalone bacterial GWAS with pyseer, independently
callable in Terra. Runs pyseer’s LMM (likelihood-ratio test) over a presence/absence Rtab,
correcting for population structure with a phylogeny-derived kinship matrix.
presence_absence_rtab is deliberately generic: pyseer’s own docs describe the Rtab format
it accepts via --pres as usable “flexibly to represent variants from other sources” — a
block_id x sample 0/1 matrix, nothing g
This is a companion discussion topic for the original entry at github.com/alex-omics/microbial-genomics-wdl/pyseer_gwas