SV-plaudit: A cloud-based framework for manually curating thousands of structural variants
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Abstract
SV-plaudit is a framework for rapidly curating structural variant (SV) 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 Variant Call Format (VCF) file. As a proof of principle, nine researchers collaborated for 1 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.
Code available at https://github.com/jbelyeu/SV-plaudit
Demonstration video available at https://www.youtube.com/watch?v=ono8kHMKxDs
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Now published in GigaScience doi: 10.1093/gigascience/giy064
Jonathan R. Belyeu 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan R. BelyeuThomas J. Nicholas 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas J. NicholasBrent S. Pedersen 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google …
Now published in GigaScience doi: 10.1093/gigascience/giy064
Jonathan R. Belyeu 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jonathan R. BelyeuThomas J. Nicholas 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas J. NicholasBrent S. Pedersen 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Brent S. PedersenThomas A. Sasani 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas A. SasaniJames M. Havrilla 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephanie N. Kravitz 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stephanie N. KravitzMegan E. Conway 1Department of Human Genetics, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteBrian K. Lohman 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UTFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Brian K. LohmanAaron R. Quinlan 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT3Department of Biomedical Informatics, University of Utah, Salt Lake City, UT+To whom correspondence should be addressedFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Aaron R. QuinlanRyan M. Layer 1Department of Human Genetics, University of Utah, Salt Lake City, UT2USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT+To whom correspondence should be addressedFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ryan M. Layer
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy064 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101187 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101188
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