Stochastic Imputation in Genomics: BEAGLE Software Overview
Explore stochastic imputation techniques in genomics, focusing on the BEAGLE software package for genotype calling, phasing, and imputation. Learn how to assign values randomly for missing data based on allele frequencies and genotype information.
Download Presentation
Please find below an Image/Link to download the presentation.
The content on the website is provided AS IS for your information and personal use only. It may not be sold, licensed, or shared on other websites without obtaining consent from the author. If you encounter any issues during the download, it is possible that the publisher has removed the file from their server.
You are allowed to download the files provided on this website for personal or commercial use, subject to the condition that they are used lawfully. All files are the property of their respective owners.
The content on the website is provided AS IS for your information and personal use only. It may not be sold, licensed, or shared on other websites without obtaining consent from the author.
E N D
Presentation Transcript
CROP 545 - LAB 4 IMPUTATION Yuanhong Song Jan 31, 2018
Emails Contain crop 545 in subject line; Homework Report in .PDF, code in .R; File name Homework2_Firstname_Lastname.pdf/.r . Textbook Full context is available through WSU Libraries online; Provides thoughts for knowledge and codes for practice. 2
Review (R) Stochastic imputation TOPICS Evaluate accuracy BEAGLE Break: 3:15 3:30 3
FILES 4
STOCHASTIC IMPUTATION Target: assign values randomly 1. For each col, calculate: fn = the sum of all genotype values fc = the number of non-zero values fa = allele frequency 2. Assign 0 or 2 randomly to each missing value U ~ unif (0,1) For all missing values: Xmis = 2 if fa < U Xmis = 0 otherwise 5
BEAGLE Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. - Author, Brian Browning https://faculty.washington.edu/browning/beagle/beagle.html 6
