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

Author:

Leung Yuk Yee1,Valladares Otto1,Chou Yi-Fan1,Lin Han-Jen1,Kuzma Amanda B1,Cantwell Laura1,Qu Liming1,Gangadharan Prabhakaran1,Salerno William J2,Schellenberg Gerard D1,Wang Li-San1

Affiliation:

1. Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Penn Neurodegeneration Genomics Center, Philadelphia, PA, USA

2. Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA

Funder

National Institute on Aging

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Reference10 articles.

1. A framework for variation discovery and genotyping using next-generation DNA sequencing data;DePristo;Nat. Genet.,2011

2. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments.;Farek;bioRxiv,2018

3. SAMBLASTER: fast duplicate marking and structural variant read extraction;Faust;Bioinformatics,2014

4. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM;Li;arXiv preprint,2013

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