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

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-plauditDemonstration video available at https://www.youtube.com/watch?v=ono8kHMKxDs.

SUBMITTER: Belyeu JR

PROVIDER: S-EPMC6030999 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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

Belyeu Jonathan R JR Nicholas Thomas J TJ Pedersen Brent S BS Sasani Thomas A TA Havrilla James M JM Kravitz Stephanie N SN Conway Megan E ME Lohman Brian K BK Quinlan Aaron R AR Layer Ryan M RM

GigaScience 20180701 7

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 ...[more]

PMID: 29860504

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