Odyssey: a Semi-Automated Pipeline for Phasing, Imputation, and Analysis of Genome-Wide Genetic Data

• NCJ Number: 254242
• Journal: Bmc Bioinformatics Volume: 20 Dated: 2019
• Author(s): Ryan. J. Eller; Sarath C. Janga; Susan Walsh
• Date Published: 2019
• Length: 9 pages
• Grant Number(s): 2015-R2-CX-0023; 2014-DN-BX-K031
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical); Report (Study/Research); Report (Grant Sponsored); Program/Project Description
• Award: Improving the prediction of human quantitative pigmentation traits such as eye, hair and skin color using a worldwide representation panel of US and European individuals; An Investigation into the genetic basis of human facial morphology and its prediction from DNA, using a globally distributed panel of individuals from the US and Europe.

Annotation

This article profiles the features and benefits for forensic science of the Odyssey pipeline, which is a simplified, efficient, semi-automated genome-wide imputation and analysis pipeline, which prepares raw genetic data, performs pre-imputation quality control, phasing, imputation, post-imputation quality control, population stratification analysis, and genome-wide association with statistical data analysis, including result visualization.

Abstract

Genome imputation, admixture resolution and genome-wide association analyses are timely and computationally intensive processes with many composite and requisite steps. Analysis time increases further when building and installing the run programs required for these analyses. For scientists that may not be as versed in programing language, but want to perform these operations hands on, there is a lengthy learning curve to utilize the vast number of programs available for these analyses. In an effort to streamline the entire process with easy-to-use steps for scientists working with big data, the Odyssey pipeline was developed. Odyssey is a pipeline that integrates programs such as PLINK, SHAPEIT, Eagle, IMPUTE, Minimac, and several R packages to create a seamless, easy-to-use, and modular workflow controlled via a single user-friendly configuration file. Odyssey was built with compatibility in mind, and thus utilizes the Singularity container solution, which can be run on Linux, MacOS, and Windows platforms. It is also easily scalable from a simple desktop to a High-Performance System (HPS). Odyssey facilitates efficient and fast genome-wide association analysis automation and can go from raw genetic data to genome: phenome association visualization and analyses results in 3-8h on average, depending on the input data, choice of programs within the pipeline and available computer resources. Odyssey was built to be flexible, portable, compatible, scalable, and easy to setup. Biologists less familiar with programing can now work hands on with their own big data using this easy-to-use pipeline. (publisher abstract modified)