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@ARTICLE{Vitale:275875,
      author       = {Vitale, Dan and Koretsky, Mathew J and Kuznetsov, Nicole
                      and Hong, Samantha and Martin, Jessica and James, Mikayla
                      and Makarious, Mary B and Leonard, Hampton and Iwaki,
                      Hirotaka and Faghri, Faraz and Blauwendraat, Cornelis and
                      Singleton, Andrew B and Song, Yeajin and Levine, Kristin and
                      Kumar-Sreelatha, Ashwin Ashok and Fang, Zih-Hua and Nalls,
                      Mike},
      title        = {{G}eno{T}ools: an open-source {P}ython package for
                      efficient genotype data quality control and analysis.},
      journal      = {G3: Genes, genomes, genetics},
      volume       = {15},
      number       = {1},
      issn         = {2160-1836},
      address      = {Pittsburgh, PA},
      publisher    = {Genetics Soc. of America},
      reportid     = {DZNE-2025-00110},
      pages        = {jkae268},
      year         = {2025},
      abstract     = {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.},
      keywords     = {Software / Humans / Genotype / Genome-Wide Association
                      Study: methods / Quality Control / Alzheimer Disease:
                      genetics / Parkinson Disease: genetics / Genetics,
                      Population / Computational Biology: methods / Uniform
                      Manifold Approximation and Projection (UMAP) (Other) /
                      ancestry (Other) / genotype (Other) / principal component
                      analysis (PCA) (Other) / python (Other)},
      cin          = {AG Heutink},
      ddc          = {570},
      cid          = {I:(DE-2719)1210002},
      pnm          = {354 - Disease Prevention and Healthy Aging (POF4-354)},
      pid          = {G:(DE-HGF)POF4-354},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39566101},
      pmc          = {pmc:PMC11708233},
      doi          = {10.1093/g3journal/jkae268},
      url          = {https://pub.dzne.de/record/275875},
}