Optimizing Genotype Phasing and Patriline Determination in Honeybees Through Pedigree Reconstruction

Introduction

This repository contain R scripts that optimize genotype phasing and patriline determination in honeybees through pedigree reconstruction using SIMplyBee.

If you have no experience with SIMplyBee, we suggest you go to the software's website simplybee.info and study the tutorials. This repository uses SIMplyBee to simulate honeybee populations as described in the below manuscript and to calculate and summarise relatedness between individual honeybees.

Respository contents

The repository contains five scripts:

• SimulatedSNPArrays.R runs a SNP array with 4 SNP chip sizes, mimicking a mating station with 2 generations of honeybees. Two SNP versions are creates, those without genotyping errors and those with added genotyping errors.
• RealData_processing.R describes the processing of the real datafiles in preparation for pedigree reconstuction and further analysis
• HaplotypePO_Patrilines.R determines the haplotype parental origins, calculates gametic Mendelian sampling values and determines patriline numbers from a vcf file.
• Plotting.R processes the output data and creates plots to visualise of all Pedigree reconstruction software and Patriline numbers.