Running qpAdm in R with ADMIXTOOLS 2: a working tutorial
From genotype files to a tested model: f2 extraction, qpadm() and its output tables, the arguments that silently change results (allsnps, fudge_twice, constrained), and the protocol discipline the code will not enforce for you.
Related posts
qpAdm troubleshooting: the errors, warnings and weird outputs, decoded
Negative weights, SE 9.99, every model rejected, every model passing, infeasible popdrop rows, allsnps confusion — the standard failure gallery of qpAdm runs and what each symptom actually indicates.
3 min read
qpAdm right populations: the O9 set, its extensions, and how many outgroups to use
The canonical nine outgroups from Lazaridis 2016, the o9a and o9aamcn extensions, the arithmetic floor and the ~30-population ceiling, and the published example where one added outgroup cut standard errors threefold.
4 min read
qpAdm analysis tutorial: from a raw DNA file to a model with a p-value
A step-by-step qpAdm tutorial: check your raw file, merge it into AADR v66, choose sources and outgroups, run it in the browser or in R, and read the result.
15 min read