GWAS Pipeline
Accelerate genomic analysis, target discovery, and drug discovery by efficiently interrogating WES datasets at biobank scale with a proven Genome-wide Association Studies (GWAS) pipeline platform
Genome-wide association studies (GWAS) are both a science and an art – no two studies are the same and cohorts need to be carefully designed. However, streamlining GWAS with a platform-based approach can improve efficiencies and avoid recurring challenges. These include:
- Standing up the infra and tech stacks needed: IT teams still take months to get the setup right even in this age of cloud computing as the expertise required cuts across many disciplines
- Scaling tech stack to handle ever-expanding datasets: UK Biobank WES dataset currently provides 300k sequences and is growing further
- Consistently applying best-practice checks for Sample and Variant QC, and screening for relatedness and other sampling biases
- Joining with a number of reference databases such as GNOMAD for allele frequencies and ClinVar for known consequences and impact
- Interactive visualization of sequence data, phenotype data and study results: This is a challenge given the size of sequence data and variety of phenotypic data
Our Solution
AI powered drug discovery platform for genomic analysis
Aganitha provides an in silico platform for GWAS, that is:
- Available on-demand, powered by Infrastructure as Code approach, supporting both in-house HPC as well as all Cloud based clusters
- Cost-effective, without dependence on expensive proprietary big data stacks and services
- Vertically integrated to provide industry leading performance
- Comprehensive, spanning all activities from data ingestion to QC, cohort selection, regression and visualization
- Interactive, enabling scientists to inspect and apply Sample and Variant QCs, and carefully design study cohorts
- Pre-integrated with commonly needed reference datasets, annotation and visualization tools
- Complemented by a complete portfolio of service offerings from Aganitha which seamlessly integrate all the genomics and technology expertise needed
Highlights
Key components & strengths
Kubernetes
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
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
Pre-Integrated
Comes pre-integrated with leading open source libraries and tools such as VEP
Services
Complemented by a complete portfolio of service offerings which seamlessly integrate all the genomics and technology expertise needed
Outcomes
Accelerated Drug Discovery with efficient & faster Genomic Analysis, GWAS, and Target Discovery
Careful cohort selections
Understand mendelian violations in trios; prune variants in linkage disequilibrium; analyze genetic similarity between samples and compute sample scores and variant loadings using PCA
Rich association studies
Perform variant, gene-burden and eQTL association analyses using linear, logistic, and linear mixed regression; estimate heritability
Industrial strength
Robust high-performance solution for your GWAS needs, that puts you firmly in control with minimal expense
Access to expertise
Augment the capacity available for setup and analysis with services from Aganitha
Instant ignition
Reduction in setup time from months to days
Scalable
Elastically scale your deployment as your WES datasets grow in size
Discover our offerings across the biopharma value chain
Our Solutions
Customizable platforms and solutions across the drug discovery value chain from target discovery to therapeutic development
Read More
Our Services
Offering services in computational sciences and technology to complement biopharma R&D
Case Studies
Helping clients accelerate drug discovery and development by building computational biology, computational chemistry, technology, and cloud solutions
Read More