RT Journal Article
SR Electronic
T1 VCPA: genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 327395
DO 10.1101/327395
A1 Yuk Yee Leung
A1 Otto Valladares
A1 Yi-Fan Chou
A1 Han-Jen Lin
A1 Amanda B Kuzma
A1 Laura Cantwell
A1 Liming Qu
A1 Prabhakaran Gangadharan
A1 Alzheimer’s Disease Sequencing Project (ADSP)
A1 William J Salerno
A1 Gerard D. Schellenberg
A1 Li-San Wang
YR 2018
UL http://biorxiv.org/content/early/2018/05/21/327395.abstract
AB Summary: We report VCPA, our SNP/Indel Variant Calling Pipeline and data management tool used for 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 is coded in Workflow Description Language and is fully optimized for the Amazon elastic compute cloud environment. This includes steps for processing raw sequence reads including read alignment, and all the way up to variant calling using GATK. The tracking database allows users to dynamically view the statuses of jobs running and the quality metrics reported by the pipeline. Users can thus monitor the production process and diagnose if any problem arises during the procedure. All quality metrics (>100 collected per processed genome) are stored in the database, thus facilitating users to compare, share and visualize the results. To summarize, VCPA is functional equivalent to the CCDG/TOPMed pipeline. Together with the dockerized database (also available as Amazon Machine Image), users can easily process any WGS/WES data on Amazon cloud with minimal installation.Availability: 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).Contact: yyee{at}pennmedicine.upenn.edu or lswang{at}pennmedicine.upenn.eduSupplementary information: Supplementary data are available at Bioinformatics online.