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Tool: Fast and Accurate DeepVariant on native Linux ARM64. Costs less than a piece of gum per genome

Hi Guys!

I've built a native Linux ARM64 port of DeepVariant targeting AWS Graviton3 and other Neoverse V1 servers. Now it can run natively on literally anything. It could even run on an android phone, but I don't recommend it since you'll be waiting a while. at $0.33/genome using an arm64 server, I believe it is very likely to be one of the cheapest variant calling implementations out there.

I've verified correctness using a truth dataset. You can check the readme in the repository.

I'm looking for anyone who can run some standard benchmarks and compare F1 scores with some additional data against the x86 baseline. Also, I appreciate if you can spread the word if you like it. Google has already acknowledged the Apple Silicon MacOS version as being awesome, so I hope this will also be pretty exciting for others.

GitHub: https://github.com/antomicblitz/deepvariant-linux-arm64

Docker image ghcr.io/antomicblitz/deepvariant-arm64:v1.9.0-arm64.6

deepvariant arm64 variant-calling
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updated by cmdcolin cmdcolin • written by antoniolamb • antoniolamb

so you could do the 1000genomes (which has about 3000 genomes now) for something like 900 bucks. not bad!

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written by cmdcolin cmdcolin

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