linzhi2013 / lcwgs-guide-tutorial

Tutorials for analysis of low-coverage whole genome sequencing data

These tutorials were developed by Matteo Fumagalli, Arne Jacobs, Nicolas Lou, and Nina Overgaard Therkildsen. An earlier version was used in the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 19-22 2020

• Tutorial 1: Data processing

• Tutorial 2: Genotype and SNP calling

• Tutorial 3a: Linkage disequilibrium

• Tutorial 3b: Population structure

• Tutorial 4: Summary statistics

Acknowledgements: This course material was developed with support from an NSF grant to NOT (OCE‐1756316).

Other resources:

Please check out our beginner's guide to low-coverage whole genome sequencing.

We also maintain two GitHub repos that host a collection of scripts for the efficient high-throughput processing and analysis of lcWGS data.