Teaching

A tutorial on how to use OneMap and the accompanying software fullsibQTL.

These R Markdown files were written to accompany lectures in the course “Genetic Mapping”, taught at the University of Wisconsin-Madison in the spring of 2021.

• Part 1 introduces the package, and demonstrates how to form linkage groups using a dataset from an F1 apple population.

• Part 2 uses this same apple dataset to illustrate how recombination frequencies are estimated between biallelic SNPs, and subsequently ordered within linkage groups.

• Part 3 demonstrates why multiallelic markers are more informative in determining marker order and phase using a dataset from an F1 family of clownfish.

• Part 4 uses the F1 apple population and the genetic maps constructed using onemap to demonstrate the use of the companion QTL mapping software fullsibQTL.

A tutorial on how to use bcftools to filter VCF files prior to genetic mapping.

This shell script was written to accompany lectures in the course “Genetic Mapping”, taught at the University of Wisconsin-Madison in the spring of 2021. The tutorial can be downloaded here, and makes use of an example marker dataset.