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

TitleVCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.
Publication TypeJournal Article
Year of Publication2019
AuthorsLeung, YYee, Valladares, O, Chou, Y-F, Lin, H-J, Kuzma, AB, Cantwell, L, Qu, L, Gangadharan, P, Salerno, WJ, Schellenberg, GD, San Wang, L-
Date Published2019 05 15
KeywordsAlzheimer Disease, Data Management, Genomics, High-Throughput Nucleotide Sequencing, Humans, Software

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 (

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Alternate JournalBioinformatics
PubMed ID30351394
PubMed Central IDPMC6513159
Grant ListU01 AG032984 / AG / NIA NIH HHS / United States
U24 AG041689 / AG / NIA NIH HHS / United States
U54 AG052427 / AG / NIA NIH HHS / United States
UG3 NS104095 / NS / NINDS NIH HHS / United States