Title | VCPA: genomic Variant Calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. |
Publication Type | Journal Article |
Year of Publication | 2018 |
Authors | Leung YYee, Valladares O, Chou Y-F, Lin H-J, Kuzma AB, Cantwell L, Qu L, Gangadharan P, Salerno WJ, Schellenberg GD, San Wang L- |
Journal | Bioinformatics |
Date Published | 2018 Oct 23 |
ISSN | 1367-4811 |
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, 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. |
DOI | 10.1093/bioinformatics/bty894 |
page_expo | Internal |
Alternate Journal | Bioinformatics |
PubMed ID | 30351394 |
Grant List | U01 AG032984 / AG / NIA NIH HHS / United States U54 AG052427 / AG / NIA NIH HHS / United States |
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