ntRoot: Genetic Ancestry Inference Across Diverse Genomic Data Types

Genetic ancestry is encoded in our genomes, reflecting the genealogical history of individuals and populations. This information is increasingly recognized as an important variable in large-scale population studies, where it is used to correct for population stratification, as well as in clinical applications, since disease risk can vary across populations. However, many studies either fail to account for ancestry, or rely on self-reported ancestry, which is often incomplete or inconsistent. Most cohort-level studies utilize single-nucleotide polymorphism (SNP) arrays, whole exome sequencing (WES), or whole genome sequencing (WGS), all of which capture genetic variation informative of ancestry. Therefore, there is great value in inferring ancestry directly from these heterogeneous data types. Previously, we developed ntRoot, a scalable tool for inferring global and local ancestry from WGS reads or assembled genomes. In newer releases, we expanded the utility of ntRoot to also infer ancestry from WES and SNP array data, making the tool flexible and robust to the wide diversity of sequencing- and array-based data used in large-scale genetics studies. The streamlined execution of ntRoot enables fast (<70 min for the ntRoot step of each protocol) and scalable ancestry inference across a wide variety of research workflows. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Running ntRoot with WGS data Basic Protocol 2: Running ntRoot with assembled genomes Basic Protocol 3: Running ntRoot with WES data Basic Protocol 4: Running ntRoot with Illumina SNP array data Basic Protocol 5: Running ntRoot with variant call format files from variant calling pipelines Support Protocol: Installing dependencies for the Basic Protocols.