GWAS Pipeline

Accelerate genomic analysis, target discovery, and drug discovery by efficiently interrogating WES datasets at biobank scale, building a customized pipeline for Genome-wide Association Studies (GWAS), and analyzing data to provide you insights

Streamlining GWAS Analysis for Deeper Insights into Complex Traits

Example - Manhattan plot: The variants (SNPs) with the strongest associations have the greatest negative logarithms, and tower over the background of unassociated SNPs
Manhattan plot depicting the strength of association between genetic SNPs across the genome and a particular trait or disease.

With several disorders finding their genetic causes through genome-wide association studies (GWAS), scientists are closer than ever to deciphering disease mechanisms, and advancing drug development. However, navigating GWAS analysis presents several bottlenecks such as case-control imbalance, sheer volume of data, statistical noise, population stratification bias, and lack of standardized methods, etc. 
Aganitha offers a GWAS pipeline designed to address your needs. We provide a comprehensive solution designed to streamline your research workflow with:

  • Data engineering:
    We employ robust data engineering techniques to ensure your genomic data adheres to the best possible quality standards for GWAS analysis. This includes stringent quality control measures and data formatting tailored to the pipelines’ algorithms.
  • Intuitive Interface:
    We prioritize a user-centric design with a simple and intuitive interface. This allows your researchers to focus on scientific inquiry and expedite their research by minimizing time spent on software manipulation.

Explore our GWAS pipeline and understand how we can help to expedite your discoveries, optimize data analytics, and gain deeper insights.

Our Solution

You can accelerate your disease studies using our GWAS platform for genomic analysis

The following our some key features of our pipeline:
  • Available on-demand: Enabling you to access our pipeline that is powered by the Infrastructure as Code approach, supporting both in-house HPC as well as all Cloud-based clusters.
  • Cost-effective: Minimizing your expenses by avoiding dependence on expensive proprietary big data stacks and services.
  • Comprehensive: Spanning all activities from data ingestion and QC to cohort selection, regression, and visualization. This puts you in complete control of your analysis, all within a secure environment.
  • Interactive Empowering your scientists to participate actively in the analysis. They can inspect and apply relevant sample and variant QCs, meticulously design study cohorts, and gain deeper insights from their data.
  • Offers seamless expertise: Ensuring comprehensive support throughout your analysis process by leveraging Aganitha’s extensive genomics and technology expertise. Our team becomes an extension of yours, assisting you towards successful outcomes.
  • Streamlined Resources Streamlining your analysis workflows by providing ready access to essential reference datasets, annotation, and visualization tools.
Given a population consisting of individuals with and without disease of interest, the steps involved are whole exome/genome sequencing, within Hail - variant analysis, quality control, LD pruning and statistical analysis followed by downstream analysis
Aganitha's GWAS Pipeline

Challenges addressed

At Aganitha, we recognize and understand the complexities that can hinder your progress in GWAS research. We take these challenges head-on and empower your research success. Some of these challenges include:

Customization Needs:

One-size-fits-all solutions rarely succeed. Your data is unique, and so are your analysis requirements. Our expertise in customization allows us to tailor each tool precisely to your specific needs. This unlocks deeper insights and empowers you to achieve research goals with exceptional precision.

Data Compatibility:

Your genomic data is a valuable asset. Proprietary data and diverse datasets can raise compatibility issues. Our team specializes in navigating complexities and ensures our tools remain compatible and effective across various datasets, securing your data while maximizing its utility.

Infrastructure Integration:

Your research is unique and the technology environment is exceptional. Integrating new tools seamlessly can be cumbersome . We ensure that our tools adapt to your specific infrastructure, guaranteeing smooth transitions and enhanced performance for your team.

Usability Hurdles:

Complex tools can hinder progress. You need help with usability issues, especially with tools that are overly sensitive to input. We prioritize user-friendliness. Our intuitive interfaces empower your team to maximize efficiency and productivity.

Maximize Genetic Insights with Aganitha's Services

Targeted Cohorts

You define the research question. We meticulously curate cohorts tailored to your objectives, ensuring precise and relevant genetic analyses. This leads to more meaningful results that propel your research forward.

Deeper Insights

Dive deep into genetic associations with confidence. Our comprehensive analyses, including variant, gene-burden, and eQTL association studies, provide you with rich insights into genetic relationships and heritability.

Empowered Research

Amplify your research capabilities by leveraging Aganitha’s expertise. Our dedicated team augments your setup and analysis, providing invaluable support and guidance every step of the way.

Accelerated Target Discovery

Our high-performance solution delivers exceptional results while putting you in control. This combination of industrial-strength capabilities and affordability allows you to ignite your research instantly, transforming months of setup into just days and accelerating your path to discovery.

Key components & strengths


Easily deployable on any cloud that supports Kubernetes, including AWS/GCP/Azure

HPC deployment with SLURM/SGE/equivalent scheduler

Deployable in internal HPC clusters using any of the leading schedulers such as SLURM, SGE
Hail on Spark

Hail on Spark

Leverages leading GWAS library, Hail (from Broad Institute), which in turn, leverages distributed data processing capabilities of Apache Spark

Jupyter notebooks

Supports interactive use by scientists, via Jupyter notebooks


Comes pre-integrated with leading open source libraries and tools such as VEP


Complemented by a complete portfolio of service offerings which seamlessly integrate all the genomics and technology expertise needed

Discover our offerings across the biopharma value chain

Learn more about our GWAS Pipeline