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SV-plaudit: A cloud-based framework for manually curating thousands of structural variants
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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030999/ https://www.ncbi.nlm.nih.gov/pubmed/29860504 http://dx.doi.org/10.1093/gigascience/giy064 |
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author | Belyeu, Jonathan R Nicholas, Thomas J Pedersen, Brent S Sasani, Thomas A Havrilla, James M Kravitz, Stephanie N Conway, Megan E Lohman, Brian K Quinlan, Aaron R Layer, Ryan M |
author_facet | Belyeu, Jonathan R Nicholas, Thomas J Pedersen, Brent S Sasani, Thomas A Havrilla, James M Kravitz, Stephanie N Conway, Megan E Lohman, Brian K Quinlan, Aaron R Layer, Ryan M |
author_sort | Belyeu, Jonathan R |
collection | PubMed |
description | 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 |
format | Online Article Text |
id | pubmed-6030999 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-60309992018-07-10 SV-plaudit: A cloud-based framework for manually curating thousands of structural variants Belyeu, Jonathan R Nicholas, Thomas J Pedersen, Brent S Sasani, Thomas A Havrilla, James M Kravitz, Stephanie N Conway, Megan E Lohman, Brian K Quinlan, Aaron R Layer, Ryan M Gigascience Research 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 Oxford University Press 2018-05-31 /pmc/articles/PMC6030999/ /pubmed/29860504 http://dx.doi.org/10.1093/gigascience/giy064 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Belyeu, Jonathan R Nicholas, Thomas J Pedersen, Brent S Sasani, Thomas A Havrilla, James M Kravitz, Stephanie N Conway, Megan E Lohman, Brian K Quinlan, Aaron R Layer, Ryan M SV-plaudit: A cloud-based framework for manually curating thousands of structural variants |
title | SV-plaudit: A cloud-based framework for manually curating thousands of structural variants |
title_full | SV-plaudit: A cloud-based framework for manually curating thousands of structural variants |
title_fullStr | SV-plaudit: A cloud-based framework for manually curating thousands of structural variants |
title_full_unstemmed | SV-plaudit: A cloud-based framework for manually curating thousands of structural variants |
title_short | SV-plaudit: A cloud-based framework for manually curating thousands of structural variants |
title_sort | sv-plaudit: a cloud-based framework for manually curating thousands of structural variants |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030999/ https://www.ncbi.nlm.nih.gov/pubmed/29860504 http://dx.doi.org/10.1093/gigascience/giy064 |
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