deepvariant

Description

deepvariant website

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

This module sets the following environment variables:

Environment Modules

Run module spider deepvariant to find out what environment modules are available for this application.

Environment Variables

• HPC_DEEPVARIANT_IMAGE - path to deepvariant container image

Additional Usage Information

From a GUI session run:

$ module load deepvariant/1.6.1

$ deepvariant --helpshort

Citation

If you publish research that uses deepvariant you have to cite it as follows:

• A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology 36, 983–987 (2018). Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T. Afshar, Sam S. Gross, Lizzie Dorfman, Cory Y. McLean, and Mark A. DePristo. doi: https://doi.org/10.1038/nbt.4235

Additionally, if you are generating multi-sample calls using our DeepVariant and GLnexus Best Practices, please cite:

• Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Bioinformatics (2021). Taedong Yun, Helen Li, Pi-Chuan Chang, Michael F. Lin, Andrew Carroll, and Cory Y. McLean. doi: https://doi.org/10.1093/bioinformatics/btaa1081

Categories

biology, genomics, sequencing, machine_learning