Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda B Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, Alzheimer’s Disease Sequencing Project (ADSP), William J Salerno, Gerard D. Schellenberg, Li-San Wang
doi: https://doi.org/10.1101/327395
Yuk Yee Leung
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Otto Valladares
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yi-Fan Chou
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Han-Jen Lin
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amanda B Kuzma
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Laura Cantwell
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Liming Qu
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Prabhakaran Gangadharan
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
William J Salerno
3Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gerard D. Schellenberg
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Li-San Wang
1Penn Neurodegeneration Genomics Center, Perelman School of Medicine at the University of Pennsylvania Richards Building, D101 3700 Hamilton Walk, Philadelphia, PA, USA.
2Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, PA, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

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.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 21, 2018.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
VCPA: genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
VCPA: genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project
Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda B Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, Alzheimer’s Disease Sequencing Project (ADSP), William J Salerno, Gerard D. Schellenberg, Li-San Wang
bioRxiv 327395; doi: https://doi.org/10.1101/327395
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
VCPA: genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project
Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda B Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, Alzheimer’s Disease Sequencing Project (ADSP), William J Salerno, Gerard D. Schellenberg, Li-San Wang
bioRxiv 327395; doi: https://doi.org/10.1101/327395

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3517)
  • Biochemistry (7373)
  • Bioengineering (5355)
  • Bioinformatics (20346)
  • Biophysics (10057)
  • Cancer Biology (7787)
  • Cell Biology (11360)
  • Clinical Trials (138)
  • Developmental Biology (6456)
  • Ecology (9994)
  • Epidemiology (2065)
  • Evolutionary Biology (13368)
  • Genetics (9378)
  • Genomics (12624)
  • Immunology (7733)
  • Microbiology (19122)
  • Molecular Biology (7482)
  • Neuroscience (41189)
  • Paleontology (301)
  • Pathology (1236)
  • Pharmacology and Toxicology (2145)
  • Physiology (3187)
  • Plant Biology (6885)
  • Scientific Communication and Education (1277)
  • Synthetic Biology (1901)
  • Systems Biology (5332)
  • Zoology (1091)