TY  - JOUR
AU  - Vitale, Dan
AU  - Koretsky, Mathew J
AU  - Kuznetsov, Nicole
AU  - Hong, Samantha
AU  - Martin, Jessica
AU  - James, Mikayla
AU  - Makarious, Mary B
AU  - Leonard, Hampton
AU  - Iwaki, Hirotaka
AU  - Faghri, Faraz
AU  - Blauwendraat, Cornelis
AU  - Singleton, Andrew B
AU  - Song, Yeajin
AU  - Levine, Kristin
AU  - Kumar-Sreelatha, Ashwin Ashok
AU  - Fang, Zih-Hua
AU  - Nalls, Mike
TI  - GenoTools: an open-source Python package for efficient genotype data quality control and analysis.
JO  - G3: Genes, genomes, genetics
VL  - 15
IS  - 1
SN  - 2160-1836
CY  - Pittsburgh, PA
PB  - Genetics Soc. of America
M1  - DZNE-2025-00110
SP  - jkae268
PY  - 2025
AB  - GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control, and genome-wide association studies capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools' 'Ancestry' module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization specified to the user's genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIH's Center for Alzheimer's and Related Dementias and the Global Parkinson's Genetics Program, GenoTools was used to process and analyze the UK Biobank and major Alzheimer's disease and Parkinson's disease datasets with over 400,000 genotypes from arrays and 5,000 whole genome sequencing samples and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous quality control, and conducted genetic ancestry-specific genome-wide association studies to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotyping and sequencing (whole genome sequencing and exome) data with reproducible and scalable ancestry, quality control, and genome-wide association studies pipelines.
KW  - Software
KW  - Humans
KW  - Genotype
KW  - Genome-Wide Association Study: methods
KW  - Quality Control
KW  - Alzheimer Disease: genetics
KW  - Parkinson Disease: genetics
KW  - Genetics, Population
KW  - Computational Biology: methods
KW  - Uniform Manifold Approximation and Projection (UMAP) (Other)
KW  - ancestry (Other)
KW  - genotype (Other)
KW  - principal component analysis (PCA) (Other)
KW  - python (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:39566101
C2  - pmc:PMC11708233
DO  - DOI:10.1093/g3journal/jkae268
UR  - https://pub.dzne.de/record/275875
ER  -