Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 May 15;35(10):1768-1770.
doi: 10.1093/bioinformatics/bty894.

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project

Yuk Yee Leung  1 , Otto Valladares  1 , Yi-Fan Chou  1 , Han-Jen Lin  1 , Amanda B Kuzma  1 , Laura Cantwell  1 , Liming Qu  1 , Prabhakaran Gangadharan  1 , William J Salerno  2 , Gerard D Schellenberg  1 , Li-San Wang  1
Affiliations

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project

Yuk Yee Leung et al. Bioinformatics. .

Erratum in

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.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
(A) VCPA tracking database; (B) dynamic view of job status; (C) VCPA Pipeline overview
See this image and copyright information in PMC

References

    1. Chandran S., et al. (2018) uBAM-unmapped BAM format, https://software.broadinstitute.org/gatk/documentation/article?id=11008.
    1. DePristo M.A., et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491–498. - PMC - PubMed
    1. Farek J., et al. (2018) xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. bioRxiv, doi: 10.1101/295071. - PMC - PubMed
    1. Faust G.G., Hall I.M. (2014) SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics, 30, 2503–2505. - PMC - PubMed
    1. Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint, 1303, 3997.

Publication types