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Large-scale copy number estimation in alfalfa mapping population using DArTag genotyping data

This tutorial introduces Qploidy2 demonstrating a typical workflow for ploidy and aneuploidy estimation using the Qploidy2 R package. We will cover data import, standardization, model...

Ploidy and Aneuploidy Estimation Using SNP Markers

This tutorial introduce Qploidy package features. The first version of the package provides a standardization method for read counts (or intensities if genotyping platform is...

Building Linkage Map for Inbred Diploid Populations with OneMap

This tutorial will show how to build a linkage map for inbred lines populations using the most updated methods implemented in OneMap 3.0.

Genotyping-by-Sequencing data SNP and dosage calling

Here we use Docker/singularity containers to perform SNP calling with GATK. We also show how to run a Workflow Description Language (WDL) to perform the...

SNP and genotype calling - A practical guide

Here we use Docker containers to perform SNP calling with GATK.Before start, it is important to highlight that all software here presented has several parameters...