Mutation Calling Agent
Omi's specialised co-pilot for mutation calling work
I call variants — SNVs, indels, mitochondrial mutations, and copy-number changes — directly from your single-cell data. Perfect for clonal tracking in cancer, mosaicism studies, or anyone who wishes their scRNA-seq could pull double duty as a genotyping experiment.
What I can do for you
I run cellSNP-lite, vartrix, or scAllele on your BAMs to genotype known variants per cell, then hand off to Vireo or Souporcell to demultiplex pooled samples or assign cells to clones.
I detect mitochondrial mutations with mgatk or MAESTER pipelines, build clonal trees, and overlay them on your transcriptomic UMAP — so you can see if your TP53-mutant clone is also the one expressing the EMT signature.
I infer copy-number alterations with inferCNV, copyKAT, or numbat, separate malignant from normal cells, and flag subclones with distinct CNV profiles.
I link mutations back to expression: differential expression between mutant and wildtype cells in the same cluster, lineage tracing across timepoints, and clean visualizations that actually fit on a slide.
Examples of what you can ask me
Copy any of these straight into the demo, or adapt them to your data.
- 1"Genotype my cells for the top 50 cancer hotspot mutations."
- 2"Demultiplex this pooled sample using natural genetic variation."
- 3"Build a mitochondrial clonal tree and overlay it on my UMAP."
- 4"Run inferCNV and separate malignant from normal cells."
- 5"Compare expression between TP53-mutant and wildtype tumor cells."
- 6"Are there subclones in my AML sample? Show me their lineage."
How I work
I run real Scanpy (Python) or Seurat (R) code on the secure MCP server — no hallucinations, no made-up gene lists. Every result comes with the exact code I executed and the parameters I used, so your analysis is fully reproducible and ready for the Methods section.
Best for
Cancer single-cell researchers, lineage-tracing folks, anyone working with pooled patient samples, and labs doing developmental mosaicism or clonal hematopoiesis studies.
References
- cellSNP-lite & Vireo (Huang & Huang, 2021) – Bioinformatics
- Souporcell (Heaton et al., 2020) – Nature Methods
- vartrix (10x Genomics)
- mgatk / MAESTER (Lareau et al., 2021; Miller et al., 2022) – Nature Biotechnology
- inferCNV (Tickle et al., Trinity CTAT)
- copyKAT (Gao et al., 2021) – Nature Biotechnology
- Numbat (Gao et al., 2023) – Nature Biotechnology
Try Mutation Calling now
Jump into the demo with a starter prompt already loaded. Upload your data, or play with our example dataset first.