Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes.

ABSTRACT: Population scale sequencing of whole human genomes is becoming economically feasible; however, data management and analysis remains a formidable challenge for many research groups. Large sequencing studies, like the 1000 Genomes Project, have improved our understanding of human demography and the effect of rare genetic variation in disease. Variant calling on datasets of hundreds or thousands of genomes is time-consuming, expensive, and not easily reproducible given the myriad components of a variant calling pipeline. Here, we describe a cloud-based pipeline for joint variant calling in large samples using the Real Time Genomics population caller. We deployed the population caller on the Amazon cloud with the DNAnexus platform in order to achieve low-cost variant calling. Using our pipelin

SUBMITTER: Shringarpure SS 

PROVIDER: S-EPMC4482534 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature