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

Dataset type: Software, Genome-Mapping
Data released on May 18, 2018

Belyeu JR; Nicholas TJ; Pedersen BS; Sasani TA; Havrilla JM; Kravitz SN; Conway ME; Lohman BK; Quinlan AR; Layer RM (2018): Supporting data for "SV-plaudit: A cloud-based framework for manually curating thousands of structural variants" GigaScience Database. http://dx.doi.org/10.5524/100450

DOI10.5524/100450

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.

Additional details

Read the peer-reviewed publication(s):

Belyeu, J. R., Nicholas, T. J., Pedersen, B. S., Sasani, T. A., Havrilla, J. M., Kravitz, S. N., … Layer, R. M. (2018). SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. GigaScience, 7(7). doi:10.1093/gigascience/giy064

Additional information:

https://github.com/jbelyeu/SV-plaudit

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
NA128789606HumanhumanHomo sapiens Description:Genomic DNA of daughter used in trio a...
Isolation source:peripheral vein
Cell type:B-Lymphocyte
...
+
NA128919606HumanhumanHomo sapiens Description:Genomic DNA of father used in trio ana...
Isolation source:peripheral vein
Cell type:B-Lymphocyte
...
+
NA128929606HumanhumanHomo sapiens Description:Genomic DNA of mother used in trio ana...
Isolation source:peripheral vein
Cell type:B-Lymphocyte
...
+
Displaying 1-3 of 3 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT1.8 KB2018-05-08
Structural variationVCF1.01 MB2018-05-08
otherTAR110.59 MB2018-05-08
scriptUNKNOWN10.73 KB2018-05-08
Tabular DataCSV2.1 MB2018-05-08
Structural variationVCF1.04 MB2018-05-08
TextTEXT1.12 KB2018-05-08
GitHub archivearchive1.45 MB2018-05-08
Displaying 1-8 of 8 File(s).
Funding body Awardee Award ID Comments
National Human Genome Research Institute RM Layer NIH K99HG009532
National Human Genome Research Institute AR Quinlan NIH R01HG006693
National Human Genome Research Institute AR Quinlan NIH R01GM124355
National Cancer Institute AR Quinlan NIH U24CA209999
Date Action
May 18, 2018 Dataset publish
May 18, 2018 File readme.txt updated
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy064