Difference between revisions of "Deepvariant"

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==System Variables==
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==

Revision as of 17:56, 14 July 2022


deepvariant website  

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

Environment Modules

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

System Variables

  • HPC_DEEPVARIANT_DIR - installation directory

Additional Information

Usage: From a GUI session run:

$ module load deepvariant/1.4.0

$ deepvariant --helpshort


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