Authors: Yue Yu, Vincent Fetterley & Cassandra Elphinstone
Level: Beginner
Title: GBS tutorial
Initial created date: Jan 2025
Updated date: March 2026
This is a tutorial to walk you through how to analyze GBS data. We will cover logging into the Digital Research Alliance servers, demultiplexing, references, mapping, SNP calling and plotting your data.
Below are a list of programs that we will use in this tutorial
Perl scripts will be used to demultiplex the data
Quality check your data
Software package for mapping DNA sequences against a large reference genome
A genomic analysis toolkit focused on variant discovery
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
dDocent is a pipeline that will walk us through building a de novo reference, mapping our reads to that reference and calling SNPs off that reference. It uses Rainbow to build the reference, and FreeBayes or GATK for SNP calling.
Admixture is a program to look at population structure. It is a good way to tell if your data has been demultiplexed correctly.
R is a programming language that we will use to run a principal component analysis and plot our data. Libraries needed include: ggplot2,
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Population genomics analyses: https://github.com/celphin/Population_genomics_Cassiope
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Genomic analysis: https://www.zoology.ubc.ca/~schluter/R/Genomics.html#SNP-calling_pipeline
Jan 31st recording - Part 2.1: Password: G?n$@=9Q
Jan 31st recording - Part 2.2: Password:*7.yVqU4