SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

Belyeu, J. R.; Nicholas, T. J.; Pedersen, B. S.; Sasani, T. A.; Havrilla, J. M.; Kravitz, S. N.; Conway, M. E.; Lohman, B. K.; Quinlan, A. R.; Layer, R. M.

doi:10.1101/265058

bioRxiv · 10.1101/265058

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

Belyeu, J. R.·Nicholas, T. J.·Pedersen, B. S.·Sasani, T. A.·Havrilla, J. M.·Kravitz, S. N.·Conway, M. E.·Lohman, B. K.·Quinlan, A. R.·Layer, R. M.

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Abstract

SV-plaudit is a framework for rapidly curating structural variant (SVs) predictions. For each SV, we generate an image that visualizes the coverage and alignment signals from a set of samples. Images are uploaded to our cloud framework where users assess the quality of each image using a client-side web application. Reports can then be generated as a tab-delimited file or annotated VCF. As a proof of principle, nine researchers collaborated for one hour to evaluate 1,350 SVs each. We anticipate that SV-plaudit will become a standard step in variant calling pipelines and the crowd-sourced curation of other biological results.\n\nCode available at https://github.com/jbelyeu/SV-plaudit\n\nDemonstration video available at https://www.youtube.com/watch?v=ono8kHMKxDs

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Belyeu, J. R., Nicholas, T. J., Pedersen, B. S., Sasani, T. A., Havrilla, J. M., Kravitz, S. N., Conway, M. E., Lohman, B. K., Quinlan, A. R., Layer, R. M.. 2018-02-14. SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. https://doi.org/10.1101/265058

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