Accurate imputation of structural and single nucleotide variants in the Atlantic salmon genome using low-coverage whole genome sequencing

Reading

Preprint available here : https://www.biorxiv.org/content/10.1101/2023.03.05.531147v1

Reference genome used in the study : ICSASG_v2

This repository contains all codes for the methods described in the preprint descibed above.

Contents

1. Reference panel generation

2. In-panel samples imputation pipeline

3. Out-panel sample SV and SNP calling

4. Out-panel samples imputation pipeline