Blog:Why we ran DeepVariant as a Nextflow pipeline over cloud.
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3.5 years ago
margarida ▴ 40

In December 2017, the team at Google Brain released an open source, deep learning based variant caller: DeepVariant (https://github.com/google/deepvariant). DeepVariant outperforms its alternatives by accuracy — it won the accuracy award at the precisionFDA Truth Challenge.

DeepVariant performs variant calling through image recognition. Running it over cloud can get quite expensive or time-consuming. However, turning it into a Nextflow (https://github.com/nextflow-io/nextflow) pipeline allows us to parallelise computations to make use of all cores of the machine and get to the results faster.

More here: https://blog.lifebit.ai/post/deepvariant/ https://github.com/lifebit-ai/DeepVariant

deepvariant cloud computing variant caller Blog • 1.9k views
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Have you benchmarked it against the actual gold standard in clinical genetics, i.e., Sanger sequencing? Why is GoogleGenomics being deprecated from Bioconductor?

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