VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.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.  VCPA is functionally equivalent to the CCDG/TOPMed pipeline.  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).



VCPA
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. 
GATK