AI Article Synopsis
- VCPA is a Variant Calling Pipeline and data management tool designed for analyzing whole genome and exome sequencing, specifically for the Alzheimer's Disease Sequencing Project.
- It consists of a pipeline for aligning sequence reads and calling variants, and a tracking database for real-time job status and quality metrics visualization, optimized for use on the Amazon cloud.
- VCPA is available for free under the MIT license, with source code and instructions accessible from the National Institute on Aging's website for academic and nonprofit use.
Article Abstract
Summary: We report VCPA, our SNP/Indel Variant Calling Pipeline and data management tool used for the analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer's Disease Sequencing Project. VCPA consists of two independent but linkable components: pipeline and tracking database. The pipeline, implemented using the Workflow Description Language and fully optimized for the Amazon elastic compute cloud environment, includes steps from aligning raw sequence reads to variant calling using GATK. The tracking database allows users to view job running status in real time and visualize >100 quality metrics per genome. VCPA is functionally equivalent to the CCDG/TOPMed pipeline. Users can use the pipeline and the dockerized database to process large WGS/WES datasets on Amazon cloud with minimal configuration.
Availability And Implementation: VCPA is released under the MIT license and is available for academic and nonprofit use for free. The pipeline source code and step-by-step instructions are available from the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (http://www.niagads.org/VCPA).
Supplementary Information: Supplementary data are available at Bioinformatics online.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513159 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/bty894 | DOI Listing |
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