STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis

If you need an accessible version of this item, please submit a remediation request.
Date
2022
Language
American English
Embargo Lift Date
Committee Members
Degree
Degree Year
Department
Grantor
Journal Title
Journal ISSN
Volume Title
Found At
Oxford University Press
Abstract

Summary: We developed the variant-Set Test for Association using Annotation infoRmation (STAAR) workflow description language (WDL) workflow to facilitate the analysis of rare variants in whole genome sequencing association studies. The open-access STAAR workflow written in the WDL allows a user to perform rare variant testing for both gene-centric and genetic region approaches, enabling genome-wide, candidate and conditional analyses. It incorporates functional annotations into the workflow as introduced in the STAAR method in order to boost the rare variant analysis power. This tool was specifically developed and optimized to be implemented on cloud-based platforms such as BioData Catalyst Powered by Terra. It provides easy-to-use functionality for rare variant analysis that can be incorporated into an exhaustive whole genome sequencing analysis pipeline.

Availability and implementation: The workflow is freely available from https://dockstore.org/workflows/github.com/sheilagaynor/STAAR_workflow.

Description
item.page.description.tableofcontents
item.page.relation.haspart
Cite As
Gaynor SM, Westerman KE, Ackovic LL, et al. STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis. Bioinformatics. 2022;38(11):3116-3117. doi:10.1093/bioinformatics/btac272
ISSN
Publisher
Series/Report
Sponsorship
Major
Extent
Identifier
Relation
Journal
Bioinformatics
Source
PMC
Alternative Title
Type
Article
Number
Volume
Conference Dates
Conference Host
Conference Location
Conference Name
Conference Panel
Conference Secretariat Location
Version
Final published version
This item is under embargo {{howLong}}