This space is home to learning materials and tutorials created for CyVerse products and services. To search the entire CyVerse wiki, use the box at the upper right.


LEARNING MATERIALS
Maintenance: Tues, 28 Jan 2020

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
 
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
 
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
 
User Portal                   8:00am to 5:00pm MST
The User Portal, http://user.cyverse.org, will be unavailable while we perform maintenance and updates.
 
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
 
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
 
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA 

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar
Check your local timezone here https://bit.ly/36iVOkX 
 
Please contact support@cyverse.org for any questions, or concerns.
 
Thank You,
CyVerse Staff 

 

 

 

 

 

 

Skip to end of metadata
Go to start of metadata


GWAS Tools

What are GWAS Tools?

Genome-Wide Association Study (GWAS) tools are resources used to examine common genetic variants in individuals to see which of those variants are associated with a given trait. For the purposes of Validate, GWAS tools are used to identify SNPs and estimate the size of their effect.

Selecting a GWAS Tool

Validate 0.9 offers several choices of GWAS tool. Should none of these GWAS tools fit to your liking, you may easily bring in your own code via iRODs or the file transfer option on the Atmosphere instance. For the sake of this tutorial, we will cover only the four main GWAS tools on the Validate Workflow:

FaST-LMM

  • Linear scalability with data size, meaning large data set analyses are not as slow as traditional GWAS tools

  • Ability to save genetic similarity matrices and other components of analysis

  • Handles epistasis and accounts for multiple confounding

  • Requires either text files or PLINK format for input

GEMMA

  • Fits univariate and multivariate linear mixed modeling for marker association with single and multiple phenotypes

  • Fits Bayesian Linear Mixed Modeling for estimating PVE by typed genotypes, predicting phenotypes, and identifying associated markers

  • Uses freely available open-source numerical libraries

  • Input files can be in PLINK or BIMBAM format

  • Optional covariate file can be included

QxPak

  • Allows IBD matrices to be included through input files

  • Offers a wide statistical modeling flexibility such as multivariate models, REML, Maximum likelihood, and BLUP estimation

  • Includes QTL analysis and also has multiQTL and multitrait modeling fully implemented

  • Custom epistasis modeling

PLINK 

  • Honestly not particularly faster or more thorough than any of the tools above

  • However, good for example analyses and file format conversion.

Each of these GWAS tools is perfectly capable for analyzing whatever dataset you may have. The next section will detail how to run everything.

Further Information

Introduction to SNPs: http://learn.genetics.utah.edu/content/pharma/snips/

The following apps have at one point been used within our workflow, but are no longer included. They can be explored via the links below:

antepi https://pods.iplantcollaborative.org/wiki/display/DEapps/AntEpiSeeker+2.0

borda count https://pods.iplantcollaborative.org/wiki/display/DEapps/Borda+Count

random jungle (which has since been turned into a program called ranger) https://pods.iplantcollaborative.org/wiki/display/DEapps/Random+Jungle+2

Icon

This tool is still in development and we are testing it currently. If you notice any issues or have any comments we would greatly appreciate them!
Please contact us at labstapleton@gmail.com. Thank you for using our tools!

  • No labels
Page: FaST-LMM Page: GEMMA Page: PLINK Page: Qxpak